Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Identification of genes associated with pistil development by transcriptome analysis of a female sterility mutant (fsm) in Chinese cabbage (Brassica campestris ssp. pekinensis)

ABSTRACT: 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.

ORGANISM(S): Brassica rapa subsp. pekinensis

SUBMITTER: Shengnan Huang

PROVIDER: E-GEOD-76917 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome Analysis of a Female-sterile Mutant (fsm) in Chinese Cabbage (Brassica campestris ssp. pekinensis).

Huang Shengnan S Liu Zhiyong Z Li Chengyu C Yao Runpeng R Li Danyang D Hou Li L Li Xiang X Liu Wenjie W Feng Hui H

Frontiers in plant science 20170410

Female-sterile mutants are ideal materials for studying pistil development in plants. Here, we identified a female-sterile mutant fsm in Chinese cabbage. This mutant, which exhibited stable inheritance, was derived from Chinese cabbage DH line 'FT' using a combination of isolated microspore culture and ethyl methanesulfonate mutagenesis. Compared with the wild-type line 'FT,' the fsm plants exhibited pistil abortion, and floral organs were also relatively smaller. Genetic analysis ...[more]

PMID: 28443127

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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 âFTâ using a combination of isolated microspore culture and radiation treatment (60Co Î³-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.

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 genes associated with pistil development by transcriptome analysis of a female sterility mutant (fsm) in Chinese cabbage (Brassica campestris ssp. pekinensis)

Publications

Transcriptome Analysis of a Female-sterile Mutant (<i>fsm</i>) in Chinese Cabbage (<i>Brassica campestris</i> ssp. <i>pekinensis</i>).

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