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

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.

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Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing

PLoS ONE ◽

10.1371/journal.pone.0153218 ◽

2016 ◽

Vol 11 (4) ◽

pp. e0153218 ◽

Cited By ~ 28

Author(s):

Fengqun Yu ◽

Xingguo Zhang ◽

Zhen Huang ◽

Mingguang Chu ◽

Tao Song ◽

...

Keyword(s):

Resistance Gene ◽

Rna Sequencing ◽

Brassica Rapa ◽

Clubroot Resistance ◽

Genome Wide ◽

Clubroot Resistance Gene

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Fine Mapping of a Clubroot Resistance Gene in Chinese Cabbage Using SNP Markers Identified from Bulked Segregant RNA Sequencing

Frontiers in Plant Science ◽

10.3389/fpls.2017.01448 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 29

Author(s):

Zhen Huang ◽

Gary Peng ◽

Xunjia Liu ◽

Abhinandan Deora ◽

Kevin C. Falk ◽

...

Keyword(s):

Resistance Gene ◽

Rna Sequencing ◽

Chinese Cabbage ◽

Fine Mapping ◽

Snp Markers ◽

Clubroot Resistance ◽

Clubroot Resistance Gene

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

10.21203/rs.3.rs-666198/v1 ◽

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.

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Fine mapping of Brassica napus blackleg resistance gene Rlm1 through bulked segregant RNA sequencing

Scientific Reports ◽

10.1038/s41598-019-51191-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Fuyou Fu ◽

Xunjia Liu ◽

Rui Wang ◽

Chun Zhai ◽

Gary Peng ◽

...

Keyword(s):

Brassica Napus ◽

Resistance Gene ◽

Rna Sequencing ◽

Catalytic Domain ◽

Leptosphaeria Maculans ◽

Snp Markers ◽

Specific Pcr ◽

Dual Specificity ◽

Kinase Catalytic Domain ◽

Allele Specific

Abstract The fungal pathogen Leptosphaeria maculans causes blackleg disease on canola and rapeseed (Brassica napus) in many parts of the world. A B. napus cultivar, ‘Quinta’, has been widely used for the classification of L. maculans into pathogenicity groups. In this study, we confirmed the presence of Rlm1 in a DH line (DH24288) derived from B. napus cultivar ‘Quinta’. Rlm1 was located on chromosome A07, between 13.07 to 22.11 Mb, using a BC1 population made from crosses of F1 plants of DH16516 (a susceptible line) x DH24288 with bulked segregant RNA Sequencing (BSR-Seq). Rlm1 was further fine mapped in a 100 kb region from 19.92 to 20.03 Mb in the BC1 population consisting of 1247 plants and a F2 population consisting of 3000 plants using SNP markers identified from BSR-Seq through Kompetitive Allele-Specific PCR (KASP). A potential resistance gene, BnA07G27460D, was identified in this Rlm1 region. BnA07G27460D encodes a serine/threonine dual specificity protein kinase, catalytic domain and is homologous to STN7 in predicted genes of B. rapa and B. oleracea, and A. thaliana. Robust SNP markers associated with Rlm1 were developed, which can assist in introgression of Rlm1 and confirm the presence of Rlm1 gene in canola breeding programs.

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Fine mapping of the clubroot resistance gene, Crr3, in Brassica rapa

Theoretical and Applied Genetics ◽

10.1007/s00122-006-0412-1 ◽

2006 ◽

Vol 114 (1) ◽

pp. 81-91 ◽

Cited By ~ 79

Author(s):

M. Saito ◽

N. Kubo ◽

S. Matsumoto ◽

K. Suwabe ◽

M. Tsukada ◽

...

Keyword(s):

Resistance Gene ◽

Brassica Rapa ◽

Fine Mapping ◽

Clubroot Resistance ◽

Clubroot Resistance Gene

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Identificaiton of a clubroot resistance locus conferring resistance to a Plasmodiophora brassicae classified into pathotype group 3 in Chinese cabbage (Brassica rapa L.)

Breeding Science ◽

10.1270/jsbbs.62.282 ◽

2012 ◽

Vol 62 (3) ◽

pp. 282-287 ◽

Cited By ~ 24

Author(s):

Takeyuki Kato ◽

Katsunori Hatakeyama ◽

Nobuko Fukino ◽

Satoru Matsumoto

Keyword(s):

Brassica Rapa ◽

Chinese Cabbage ◽

Plasmodiophora Brassicae ◽

Resistance Locus ◽

Clubroot Resistance ◽

Group 3

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

HortTechnology ◽

10.21273/horttech.22.3.311 ◽

2012 ◽

Vol 22 (3) ◽

pp. 311-319 ◽

Cited By ~ 8

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.

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Transcriptome and Coexpression Network Analyses Reveal Hub Genes in Chinese Cabbage (Brassica rapa L. ssp. pekinensis) During Different Stages of Plasmodiophora brassicae Infection

Frontiers in Plant Science ◽

10.3389/fpls.2021.650252 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuxiang Yuan ◽

Liuyue Qin ◽

Henan Su ◽

Shuangjuan Yang ◽

Xiaochun Wei ◽

...

Keyword(s):

Chinese Cabbage ◽

Plasmodiophora Brassicae ◽

Primary Root ◽

Resistance Mechanisms ◽

Coexpression Network ◽

Hub Genes ◽

Clubroot Resistance ◽

Network Analyses ◽

Cortical Infection ◽

Root Hair Infection

Clubroot, caused by the soil-borne protist Plasmodiophora brassicae, is one of the most destructive diseases of Chinese cabbage worldwide. However, the clubroot resistance mechanisms remain unclear. In this study, in both clubroot-resistant (DH40R) and clubroot-susceptible (DH199S) Chinese cabbage lines, the primary (root hair infection) and secondary (cortical infection) infection stages started 2 and 5 days after inoculation (dai), respectively. With the extension of the infection time, cortical infection was blocked and complete P. brassica resistance was observed in DH40R, while disease scales of 1, 2, and 3 were observed at 8, 13, and 22 dai in DH199S. Transcriptome analysis at 0, 2, 5, 8, 13, and 22 dai identified 5,750 relative DEGs (rDEGs) between DH40R and DH199S. The results indicated that genes associated with auxin, PR, disease resistance proteins, oxidative stress, and WRKY and MYB transcription factors were involved in clubroot resistance regulation. In addition, weighted gene coexpression network analysis (WGCNA) identified three of the modules whose functions were highly associated with clubroot-resistant, including ten hub genes related to clubroot resistance (ARF2, EDR1, LOX4, NHL3, NHL13, NAC29, two AOP1, EARLI 1, and POD56). These results provide valuable information for better understanding the molecular regulatory mechanism of Chinese cabbage clubroot resistance.

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