Exploring the genes associated with male sterility mutant (msm) in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq
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ABSTRACT:
PROVIDER: PRJNA516468 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8474140_1.fastq.gz | Fastqsanger.gz | |||
| SRR8474140_2.fastq.gz | Fastqsanger.gz | |||
| SRR8474141_1.fastq.gz | Fastqsanger.gz | |||
| SRR8474141_2.fastq.gz | Fastqsanger.gz | |||
| SRR8474142_1.fastq.gz | Fastqsanger.gz |
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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:The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line âFTâ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type âFTâ, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of âFTâ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between âFTâ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. âFTâ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage. The RNA from the developing flower buds of a female sterility mutant (fsm) and its wild typeâFTâat the full-bloom stage in Chinese cabbage were sequenced by RNA-Seq, in triplicate.
2016-06-02 | E-GEOD-76917 | biostudies-arrayexpress
Project description:We studied the causes of sterility underlying multiple-allele-inherited male sterility in Chinese cabbage by identifying differentially expressed genes (DEGs) related to pollen sterility between fertile and sterile flower buds. In this work,we performed transcriptome analysis of mRNA isolated from fertile and sterile buds using Illumina HiSeq 2000 platform sequencing. Approximately 80% of ~229 million high quality paired-end reads were uniquely mapped to the reference genome. In sterile buds, 699 genes were significantly up-regulated and 4,096 genes were down-regulated. Among the DEGs, 28 pollen cell wall-related genes, 53 transcription factor genes, 45 phytohormone-related genes, 20 anther and pollen-related genes, 212 specifically expressed transcripts (SETs), and 417 DEGs located in linkage group R07 were identified. Six transcription factor genes BrAMS, BrMS1, BrbHLH089, BrbHLH091, BrAtMYB103, and BrANAC025, were identified as putative sterility-related genes. The weak auxin signal that is regulated by BrABP1 may be one of the key factors causing pollen sterility observed here. Moreover, several significantly enriched GO terms “cell wall organization or biogenesis” (GO:0071554), “intrinsic to membrane” (GO:0031224), “integral to membrane” (GO:0016021), “hydrolase activity, acting on ester bonds” (GO:0016788) and one significantly enriched pathway “starch and sucrose metabolism” (ath00500) were obtained in this work. qRT-PCR and in situ hybridization validated that our RNA-seq transcriptome analysis was accurate and reliable. This study will lay the foundation for elucidating the molecular mechanism(s) underlying sterility, and provide valuable information for studying multiple-allele-inherited male sterility in Chinese cabbage line ‘AB01’.
2017-02-23 | GSE95242 | GEO
Project description:The female sterility mutants are ideal materials for studying the pistil development in plants. We identified a female sterility mutant (fsm) exhibiting stable inheritance, which was derived from a Chinese cabbage DH line ‘FT’ using the combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. Genetic analysis indicated that the phenotype of fsm was controlled by a single recessive nuclear gene. The morphological observations revealed that the differences in the floral organs were significant between fsm and its wild type ‘FT’, the pistil of fsm was smaller and shorter, especially the ovary; and the degenerated ovule in the ovary may directly result in the female sterility. Comparative transcriptome analysis of ‘FT’ and fsm were performed using RNA-Seq. A total of 1,872 differentially expressed genes were identified between ‘FT’ and fsm. Of these, a number of genes involved in the ovule development were found, such as PRETTY FEW SEEDS 2 (PFS2) and temperature-induced lipocalin (TIL), and these genes were all up-regulated in the fsm vs. ‘FT’ comparison. Furthermore, GO and KEGG pathway enrichment analyses of DEGs suggested a variety of biological processes and metabolic pathways were significantly enriched during the pistil development. In addition, the expression patterns of eighteen DEGs were analyzed using qRT-PCR to confirm the accuracy of the RNA-seq data. A total of 31,272 single nucleotide polymorphisms (SNPs) were specifically detected in fsm, which could be directly related to the female sterility phenotype. These results contribute to increase our understanding of the molecular mechanisms of pistil development in Chinese cabbage.
2016-06-02 | GSE76917 | GEO
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:Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). These data were then used to construct competitive endogenous RNA (ceRNA) networks, which can provide valuable information for better understanding the mechanism of leaf and petiole development. Results: In this study, the leaf and petiole of the baby Chinese cabbage inbred line ‘PHL’ were used as research materials for whole-transcriptome sequencing. A total of 10646 differentially expressed (DE) mRNAs, 303 DE lncRNAs, 7 DE circRNAs, and 195 DE miRNAs were identified between the leaf and petiole. Some transcription factors or proteins that play important roles in leaf and petiole development were identified, such as xyloglucan endotransglucosylase/hydrolase (XTH) protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, cellulose synthase (CESA), MOR1-like protein, and plant hormone biosynthesis related genes. Additionally, we constructed a leaf and petiole development-related ceRNA regulatory network, and obtained 85 pairs of ceRNA relationships, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA and 2 DEmiRNA-DEcircRNA. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaf and petiole of baby Chinese cabbage were screened from transcriptome data for subcellular localization analysis and overexpression transgenic verification. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoprotein and BrLSH2 has an obvious inhibitory effect on the growth and development of Arabidopsis thaliana. Conclusions: Our results revealed the potential mRNAs and non-coding RNAs (ncRNAs) involved in leaf and petiole development, which laid a foundation for further research on the molecular mechanism of leaf and petiole development in Chinese cabbage.
2022-12-29 | GSE218959 | GEO
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:Using 300K′-high density microarray covering the chinese cabbage whole genome, genome-wide expression analyses of cold stress conditions.
2016-10-31 | GSE75145 | 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