scholarly journals Root Transcriptome and Metabolome Profiling Reveal Key Phytohormone-Related Genes and Pathways Involved Clubroot Resistance in Brassica rapa L.

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaochun Wei ◽  
Yingying Zhang ◽  
Yanyan Zhao ◽  
Zhengqing Xie ◽  
Mohammad Rashed Hossain ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Indoleacetic Acid ◽  
Defense Mechanism ◽  
Plasmodiophora Brassicae ◽  
Rna Seq ◽  
Clubroot Disease ◽  
Clubroot Resistance ◽  
Plant Pathogen Interaction ◽  
Metabolome Profiling ◽  
Transcriptomic Changes

Plasmodiophora brassicae, an obligate biotrophic pathogen-causing clubroot disease, can seriously affect Brassica crops worldwide, especially Chinese cabbage. Understanding the transcriptome and metabolome profiling changes during the infection of P. brassicae will provide key insights in understanding the defense mechanism in Brassica crops. In this study, we estimated the phytohormones using targeted metabolome assays and transcriptomic changes using RNA sequencing (RNA-seq) in the roots of resistant (BrT24) and susceptible (Y510-9) plants at 0, 3, 9, and 20 days after inoculation (DAI) with P. brassicae. Differentially expressed genes (DEGs) in resistant vs. susceptible lines across different time points were identified. The weighted gene co-expression network analysis of the DEGs revealed six pathways including “Plant–pathogen interaction” and “Plant hormone signal transduction” and 15 hub genes including pathogenic type III effector avirulence factor gene (RIN4) and auxin-responsive protein (IAA16) to be involved in plants immune response. Inhibition of Indoleacetic acid, cytokinin, jasmonate acid, and salicylic acid contents and changes in related gene expression in R-line may play important roles in regulation of clubroot resistance (CR). Based on the combined metabolome profiling and hormone-related transcriptomic responses, we propose a general model of hormone-mediated defense mechanism. This study definitely enhances our current understanding and paves the way for improving CR in Brassica rapa.

scholarly journals Identification and Characterization of Circular RNAs in Brassica rapa in Response to Plasmodiophora brassicae

2021 ◽  
Author(s):  
Huishan Liu ◽  
Chinedu Charles Nwafor ◽  
Yinglan Piao ◽  
Xiaonan Li ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Brassica Rapa ◽  
Target Genes ◽  
Zinc Finger Protein ◽  
Plasmodiophora Brassicae ◽  
Resistance Mechanisms ◽  
Circular Rnas ◽  
Clubroot Disease ◽  
Clubroot Resistance ◽  
Competing Endogenous Rnas

Abstract BackgroundPlasmodiophora brassicae is a soil-borne pathogen that attacks the roots of cruciferous plants, causing clubroot disease. CircRNAs are non-coding RNAs widely exist in plant and animal species which can acting as “microRNA (miRNA) sponges” and “competing endogenous RNAs (ceRNAs)”. Knowledge of circRNAs has been updated continuously and rapidly. However, the information about circRNAs in the regulation of clubroot-disease resistance is limited in Brassica rapa. ResultsHere, the Chinese cabbage (BJN 222) containing clubroot resistance gene (CRa) resistant to the Pb4 was susceptible to the PbE of P. brassicae. To investigate the mechanism of cicRNAs responsible for clubroot-disease resistance in Brassica rapa, the circRNA-seq was performed roots of BJN 222 at 0 d, 8 d, and 23 d after inoculated with Pb4 and PbE. A total of 1636 circRNAs were detected distributed on 10 chromosomes. Furthermore, total 231 differentially expressed circRNAs between groups were screened. Parental genes of circRNAs functions analysis results indicated that the expression of circRNAs was affected not only by inoculation time but also by the pathogenicity of P. brassicae. However, the “Phenylalanine, tyrosine, and tryptophan biosynthesis” pathway was significant enriched between the two pathotypes at different inoculation times. All the expression of target genes annotated with “receptor-like protein kinase,” “zinc finger protein,” “LRR-repeat protein,” and “hormone-related” identified from the circRNA-miRNA-mRNA network were analyzed. 5 target genes were consistent with the expression pattern of novel_circ_000495 at 8 dpi, but only Bra026508 was significantly up-regulated. ConclusionThe up-regulated novel_circ_000495 might suppressed the expression of miR5656-y, leading to the up-regulation of Bra026508. Our results provided new insights to clubroot resistance mechanisms of B.rapa and laid a foundation for further research on the function of circRNAs responsible for the pathogen infection.

Screening of Brassica germplasm for resistance to Plasmodiophora brassicae pathotypes prevalent in Canada for broadening diversity in clubroot resistance

2012 ◽  
Vol 92 (3) ◽  
pp. 501-515 ◽  
Author(s):  
Muhammad Jakir Hasan ◽  
Stephen E. Strelkov ◽  
Ronald J. Howard ◽  
Habibur Rahman
Keyword(s):  
Brassica Rapa ◽  
Oilseed Rape ◽  
Specific Resistance ◽  
Plasmodiophora Brassicae ◽  
Diploid Species ◽  
The Other ◽  
Clubroot Disease ◽  
Clubroot Resistance ◽  
Resistant Cultivars ◽  
Spring Type

Hasan, M. J., Strelkov, S. E., Howard, R. J. and Rahman, H. 2012. Screening of Brassica germplasm for resistance to Plasmodiophora brassicae pathotypes prevalent in Canada for broadening diversity in clubroot resistance. Can. J. Plant Sci. 92: 501–515. Clubroot disease of crucifers, caused by Plasmodiophora brassicae, poses a threat to the Canadian canola industry, and the development of resistant cultivars is urgently needed. Germplasm resistant to local pathotype(s) is the prime requirement for breeding clubroot-resistant cultivars. The objective of this study was to identify Brassica germplasm possessing resistance to P. brassicae pathotypes prevalent in Alberta. Pathotype-specific resistance was identified in the diploid species Brassica rapa (AA) and B. oleracea (CC), and in the amphidiploid B. napus (AACC). Among B. rapa genotypes, turnip was the most resistant, followed by winter type and spring type oilseed rape. The rutabaga group of B. napus, on the other hand, was homogeneous for resistance to Canadian P. brassicae pathotypes. The diploid species B. nigra (BB) also showed pathotype-specific resistance. However, the two amphidiploids carrying the B. nigra genome, B. juncea (AABB) and B. carinata (BBCC) were completely susceptible to clubroot.

scholarly journals Identification and Characterization of Crr1a, a Gene for Resistance to Clubroot Disease (Plasmodiophora brassicae Woronin) in Brassica rapa L.

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e54745 ◽  
Author(s):  
Katsunori Hatakeyama ◽  
Keita Suwabe ◽  
Rubens Norio Tomita ◽  
Takeyuki Kato ◽  
Tsukasa Nunome ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Plasmodiophora Brassicae ◽  
Clubroot Disease ◽  
Identification And Characterization

scholarly journals Effect of Host Resistance and Fungicide Application on Clubroot Pathotype 6 in Green Cabbage and Napa Cabbage

2012 ◽  
Vol 22 (3) ◽  
pp. 311-319 ◽  
Author(s):  
Catarina Saude ◽  
Alan McKeown ◽  
Bruce D. Gossen ◽  
Mary Ruth McDonald
Keyword(s):  
Brassica Oleracea ◽  
Brassica Rapa ◽  
Host Resistance ◽  
Plasmodiophora Brassicae ◽  
Field Trials ◽  
Organic Soils ◽  
Southern Ontario ◽  
Clubroot Resistance ◽  
Mineral Soils ◽  
Standard Cultivar

Field trials were conducted to evaluate resistance to clubroot (Plasmodiophora brassicae, pathotype 6) in green cabbage (Brassica oleracea var. capitata) and napa cabbage (Brassica rapa ssp. pekinensis) at sites in southern Ontario in 2009 and 2010. The reaction of green cabbage cultivars Kilaton, Tekila, Kilaxy, and Kilaherb and the commercial standard cultivars, Bronco or Atlantis, were evaluated on organic (two site-years) and mineral soils (two site-years) that were naturally infested with the clubroot pathogen. In addition, fluazinam fungicide was drench applied to one treatment of the commercial standard cultivar immediately after transplanting. The napa cabbage cultivars Yuki, Deneko, Bilko, and Mirako (in 2009) and Emiko, Mirako, Yuki, and China Gold (in 2010) were evaluated only on organic soils (two site-years). At harvest, the roots of each plant were assessed for clubroot incidence and severity. Also, plant and head characteristics of the resistant green cabbage cultivars were evaluated at one site in 2010. The green cabbage cultivars Kilaton, Tekila, Kilaxy, and Kilaherb were resistant to pathotype 6 (0% to 3.8% incidence), but ‘Bronco’ was susceptible (64% to 100% incidence). Application of fluazinam reduced clubroot severity on ‘Bronco’ by 6% at one of three sites. Resistance was more effective in reducing clubroot than application of fluazinam. Plant and head characteristics of the resistant cultivars were similar to those of ‘Bronco’ treated with fluazinam. Napa cabbage cultivars Yuki, Deneko, Bilko, Emiko, and China Gold were resistant to clubroot (0% to 13% incidence), and ‘Mirako’ was highly susceptible (87% to 92% incidence). We conclude that the clubroot resistance available in several cultivars of green and napa cabbage was effective against P. brassicae pathotype 6.

scholarly journals Resistance to Plasmodiophora brassicae in Brassica rapa and Brassica juncea genotypes From China

Plant Disease ◽  
2015 ◽  
Vol 99 (6) ◽  
pp. 776-779 ◽  
Author(s):  
Hui Zhang ◽  
Jie Feng ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Fei Li ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Significant Interaction ◽  
Plasmodiophora Brassicae ◽  
Inbred Lines ◽  
Vegetable Crops ◽  
Highly Pathogenic ◽  
Clubroot Disease ◽  
Pak Choi ◽  
China Development

Clubroot disease, caused by Plasmodiophora brassicae Woronin, has become a major problem in cruciferous crops worldwide. Chinese cabbage (Brassica rapa), pak choi (B. rapa), and mustard (B. juncea) are important vegetable crops in China. Development of clubroot-resistant cultivars of these crops is urgently needed. In this study, 71 B. rapa and B. juncea genotypes from China, including cultivars and inbred lines, were evaluated for resistance to three P. brassicae pathotypes. A significant interaction was observed between the P. brassicae pathotypes and the Brassica genotypes. Pathotype 3, as defined on the differentials of Williams, exhibited the weakest virulence on all plant material. By contrast, pathotypes 5 and 6 were both highly pathogenic on most of the tested genotypes. In all, 10 of the 14 Chinese cabbage cultivars were resistant to all three pathotypes, while 4 were resistant only to a specific pathotype. Seven of eight progenies obtained from the selfing of Chinese cabbage cultivars were resistant to pathotype 3 but most were susceptible to pathotypes 5 and 6. Most inbred lines of Chinese cabbage and all inbred lines of pak choi and mustard were susceptible to all three pathotypes but their susceptibility was lower to pathotype 3 than to pathotypes 5 and 6.

Identification of lncRNAs in response to infection by Plasmodiophora brassicae in Brassica napus and development of lncRNA-based SSR markers

Genome ◽  
2020 ◽  
Author(s):  
Aarohi Summanwar ◽  
Urmila Basu ◽  
Nat N. V. Kav ◽  
Habibur Rahman
Keyword(s):  
Ssr Markers ◽  
Target Genes ◽  
Plasmodiophora Brassicae ◽  
Enrichment Analysis ◽  
Pathway Enrichment Analysis ◽  
Clubroot Resistance ◽  
Spring Canola ◽  
Resistant Lines ◽  
Plant Pathogen Interaction ◽  
Dh Lines

Clubroot resistance in spring canola has been introgressed from different Brassica sources; however, molecular mechanism underlying this resistance, especially the involvement of long non-coding RNAs (lncRNAs), yet to be understood. We identified 464 differentially expressed (DE) lncRNAs from the roots of clubroot resistant canola, carrying resistance on chromosome BnaA03, and susceptible canola lines challenged with Plasmodiophora brassicae pathotype 3. Pathway enrichment analysis showed that most of the target genes regulated by these DE lncRNAs belonged to plant-pathogen interaction and hormone signaling, as well as primary and secondary metabolic pathways. Comparative analysis of these lncRNAs with the previously reported 530 DE lncRNAs, identified using resistance located on BnaA08, detected 12 lncRNAs which showed a similar trend of upregulation in both types of resistant lines; these lncRNAs probably play a fundamental role in clubroot resistance. We identified SSR markers within 196 DE lncRNAs. Genotyping of two DH populations carrying resistance on BnaA03 identified a marker capable of detecting the resistance in 98% of the DH lines. To our knowledge, this is the first report of the identification of SSRs within the lncRNAs responsive to P. brassicae infection demonstrating the potential use of the lncRNAs in the breeding of Brassica crops.

scholarly journals Transcriptome Arofile of Brassica rapa L. Reveals the Involvement of Jasmonic Acid, Ethylene, and Brassinosteroid Signaling Pathways in Clubroot Resistance

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 589 ◽  
Author(s):  
Pengyu Fu ◽  
Yinglan Piao ◽  
Zongxiang Zhan ◽  
Yuzhu Zhao ◽  
Wenxing Pang ◽  
...  
Keyword(s):  
Jasmonic Acid ◽  
Signaling Pathways ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Defense Mechanisms ◽  
Transcriptional Analysis ◽  
Post Inoculation ◽  
Clubroot Disease ◽  
Clubroot Resistance ◽  
Sa Signaling

Plasmodiophora brassicae is a protozoan pathogen that causes clubroot disease in cruciferous plants, particularly Chinese cabbage (Brassica rapa). A previous study identified a clubroot resistance gene (CRd) conferring race-specific resistance to P. brassicae. However, the defense mechanisms of B. rapa against virulent vs. avirulent P. brassicae are poorly understood. In this study, we carried out a global transcriptional analysis in the clubroot-resistant Chinese cabbage inbred line “85–74” carrying the CRd gene and inoculated with avirulent (LAB-4) or virulent (SCCD-52) P. brassicae. RNA sequencing showed that “85–74” responded most rapidly to SCCD-52 infection, and the number of differentially expressed genes was much higher in SCCD-52-treated as compared to LAB-4-treated plants (5552 vs. 304). Transcriptome profiling revealed that plant hormone signal transduction and plant–pathogen interaction pathways played key roles in the late stages of P. brassicae infection. Genes relating to the salicyclic acid (SA), jasmonic acid (JA)/ethylene (ET), and brassinosteroid (BR) signaling pathways were up-regulated relative to untreated plants in response to LAB-4 infection at 8, 16, and 32 days post-inoculation (dpi) whereas JA, ET, and BR signaling-related genes were not activated in response to SCCD-52, and SA signaling-related genes were up-regulated in both LAB-4 and SCCD-52, suggesting that SA signaling is not the key factor in host resistance to avirulent P. brassicae. In addition, genes associated with phosphorylation and Ca2+ signaling pathways were down-regulated to a greater degree following LAB-4 as compared to SCCD-52 infection at 8 dpi. These results indicate that effector-triggered immunity in “85–74” is more potently activated in response to infection with avirulent P. brassicae and that JA, ET, and BR signaling are important for the host response at the late stage of infection. These findings provide insight into P. brassicae pathotype-specific defense mechanisms in cruciferous crops.

scholarly journals Two Clubroot-Resistance Genes, Rcr3 and Rcr9wa, Mapped in Brassica rapa Using Bulk Segregant RNA Sequencing

2020 ◽  
Vol 21 (14) ◽  
pp. 5033
Author(s):  
Md. Masud Karim ◽  
Abdulsalam Dakouri ◽  
Yan Zhang ◽  
Qilin Chen ◽  
Gary Peng ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Rna Sequencing ◽  
Brassica Rapa ◽  
Plasmodiophora Brassicae ◽  
Genetic Resistance ◽  
Doubled Haploid Line ◽  
Resistance Mechanisms ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Clubroot Resistance

Genetic resistance is widely used to manage clubroot (Plasmodiophora brassicae) in brassica crops, but new pathotypes have recently been identified on canola (Brassica napus) on the Canadian prairies. Resistance effective against both the most prevalent pathotype (3H, based on the Canadian Clubroot Differential system) and the new pathotypes is needed. BC1 plants of Brassica rapa from a cross of line 96-6990-2 (clubroot resistance originating from turnip cultivar ‘Waaslander’) and a susceptible doubled-haploid line, ACDC, exhibited a 1:1 segregation for resistance against pathotypes 3H and 5X. A resistance gene designated as Rcr3 was mapped initially based on the percentage of polymorphic variants using bulked segregant RNA sequencing (BSR-Seq) and further mapped using Kompetitive Allele Specific PCR. DNA variants were identified by assembling short reads against a reference genome of B. rapa. Rcr3 was mapped into chromosome A08. It was flanked by single nucleotide polymorphisms (SNP) markers (A90_A08_SNP_M12 and M16) between 10.00 and 10.23 Mb, in an interval of 231.6 Kb. There were 32 genes in the Rcr3 interval. Three genes (Bra020951, Bra020974, and Bra020979) were annotated with disease resistance mechanisms, which are potential candidates for Rcr3. Another resistance gene, designated as Rcr9wa, for resistance to pathotype 5X was mapped, with the flanking markers (A90_A08_SNP_M28 and M79) between 10.85 and 11.17 Mb using the SNP sites identified through BSR-Seq for Rcr3. There were 44 genes in the Rcr9wa interval, three of which (Bra020827, Bra020828, Bra020814) were annotated as immune-system-process related genes, which are potential candidates for Rcr9wa.

Sign in / Sign up

Export Citation Format

Share Document