Multi-omics profiling elucidates defense-related pathways and metabolites against clubroot in Chinese cabbage
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PROVIDER: PRJNA1321891 | ENA |
REPOSITORIES: ENA
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Project description:Clubroot disease, caused by Plasmodiophora brassicae Woronin, leads to substantial yield losses in Brassica crops worldwide, including Chinese cabbage. Nevertheless, the molecular mechanisms underlying host defense responses remain poorly understood. In this study, we assessed clubroot resistance by comparing the resistant line ‘CR Jingqiu Xinsanhao’ (JQX3) with the susceptible cultivar ‘Zhongbai 76’ (ZB76) through histological analysis of root tissues and monitoring of disease progression in pot trials. Integrated transcriptomic and metabolomic approaches were employed to characterize the defense mechanisms of JQX3 against P. brassicae infection. Marked metabolic reprogramming was detected during both the primary (3 days after inoculation, DAI) and secondary (10 DAI) infection stages. Four pathways—tyrosine metabolism, phenylpropanoid biosynthesis, valine, leucine and isoleucine biosynthesis, and glucosinolate biosynthesis—were significantly enriched at both time points. Notably, differential expression of key enzymatic genes and accumulation of intermediates in the lignin biosynthesis pathway underscored the importance of lignification in the JQX3–P. brassicae interaction. Furthermore, the intermediates p-coumaric acid and coniferaldehyde markedly inhibited P. brassicae spore germination, demonstrating their direct antifungal activity and potential as natural agents for disease control. These findings elucidate key defense-related pathways in Chinese cabbage and offer valuable insights for the development of sustainable clubroot management strategies.
2025-09-14 | GSE307500 | GEO
Project description:Pectobacterium carotovorum ssp. carotovorum (Pcc) is a necrotrophic bacterial species that causes soft rot disease in Chinese cabbage. In this study, plants harboring the resistant mutant sr gene, which confers resistance against Pcc,were screened from an 800 M2 population mutated by ethyl methane sulfonate (EMS) and scored in vitro and in vivo for lesion size. The transcript profiles showed ~512 differentially expressed genes (DEGs) between sr and WT plants occurring between 6 and 12 h postinoculation (hpi), which corresponded to the important defense regulation period (resistance) to Pcc in Chinese cabbage. The downstream defense genes (CPK, CML, RBOH MPK3, and MPK4) of pathogen pattern-triggered immunity (PTI) were strongly activated during infection at 12 hpi in resistant mutant sr; PTI appears to be central to plant defense against Pcc via recognition by three putative pattern recognition receptors (PRRs; BrLYM1-BrCERK1, BrBKK1/SERK4-PEPR1, BrWAKs). Pcc triggered the upregulation of the jasmonic acid (JA) and ethylene (ET) biosynthesis genes in mutant sr, but auxins and other hormones may have affected some negative signals.Endogenous hormones (auxins, JAs, and SA), as well as exogenous auxins (MEJA and BTH), were also verified as functioning in the immune system. Concurrently, the expression of glucosinolate and lignin biosynthesis genes was increased at 12 hpi in resistant mutant sr, and the accumulation of glucosinolate and lignin also indicated that these genes have a functional defensive role against Pcc. Our study provides valuable information and elucidates the resistance mechanism of Chinese cabbage against Pcc infection.
2022-07-27 | GSE209906 | GEO
Project description:Comparative transcriptome analysis reveals defense responses against soft rot in Chinese cabbage
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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:Identification of Chinese cabbage genes up-regulated by prolonged cold by using cDNA microarray.
2006-10-25 | E-MEXP-190 | biostudies-arrayexpress
Project description:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio â¥1, false discovery rate â¤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to âmetabolic pathwaysâ (333 members), âribosomeâ (314 members), âbiosynthesis of secondary metabolitesâ (218 members), âplant-pathogen interactionâ (146 members), and âplant hormone signal transductionâ (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment. Transcriptomic analysis of MeJA-treated Chinese cabbage leaf
2015-12-31 | E-GEOD-51363 | biostudies-arrayexpress
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:We conducted a RNA-Seq analysis of MeJA-treated Chinese cabbage leaf transcriptome. Total 14,619,469 sequence reads were generated to produce 27,461 detected genes, among which 1,451 genes were up-regulated and 991 genes were down-regulated as differentially expressed genes (DEGs) (log2 ratio ≥1, false discovery rate ≤0.001). More than 90% of the DEGs (2,278) were between 1.0- and 3.0-fold (log2 ratio). The most highly represented pathways by 1,674 annotated DEGs were related to “metabolic pathways” (333 members), “ribosome” (314 members), “biosynthesis of secondary metabolites” (218 members), “plant-pathogen interaction” (146 members), and “plant hormone signal transduction” (99 members). Fourteen genes involved in JA biosynthesis pathway were up-regulated. As many as 182 genes for the biosynthesis of several secondary metabolites were induced, and the level of indole glucosinolate was highly increased by MeJA treatment. The genes encoding sugar catabolism and some amino acids synthesis were up-regulated, which could supply structural intermediates and energy for the biosynthesis of secondary metabolites. The results demonstrated a high degree of transcriptional complexity with dynamic coordinated changes in global gene expression of Chinese cabbage in response to MeJA treatment. It expands our understanding of the complex molecular events on JA-induced plant resistance and accumulation of secondary metabolites. It also provides a foundation for further studies on the molecular mechanisms of different pathways in other Brassica crops under MeJA treatment.
2015-12-31 | GSE51363 | 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:Next-generation sequencing has been applied on seedling of two genotypes of noheading Chinese cabbage, Huaq and Wut. The goals of this study are to compare the different expression of small RNAs which is possible effect the phynotype of close genetic relation cultivars.
2014-06-14 | GSE38722 | GEO