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Phenotypes of the Brassica rapa parents: Chinese cabbage cv. “Jazz” (R) and susceptible canola breeding line ACDC. Plants were inoculated with pathotype 3 of Plasmodiophora brassicae.
Source publication
Clubroot, caused by Plasmodiophora brassicae, is an important disease of canola (Brassica napus) in western Canada and worldwide. In this study, a clubroot resistance gene (Rcr2) was identified and fine mapped in Chinese cabbage cv. “Jazz” using single-nucleotide polymorphisms (SNP) markers identified from bulked segregant RNA sequencing (BSR-Seq)...
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Clubroot caused by Plasmodiophora brassicae poses a serious threat to canola production around the world, but sources of clubroot resistance in canola are limited. In this study, turnip cultivar “Purple Top White Globe,” which is highly resistant to pathotype 3 (Williams’ system), was used as the source of resistance. Genetic studies showed that th...
Citations
... Most of the clubroot resistant (CR) loci are isolated from B. rapa, B. oleracea and mostly from the A genome. Some of the identified CR loci include PbBa1.1 and Crr2 from A01chromosome (Suwabe et al., 2003;Chen et al., 2013), CRc and Rcr8 from A02 chromosome, and the maximum number of 16 from the A03 chromosome [PbBa3.1 (Chen et al., 2013), PbBa3.2 (Chen et al., 2013), Crr3 (Hirai et al., 2004), CRk (Sakamoto et al., 2008), CRd (Pang et al., 2018), PbBa3.3 (Chen et al., 2013), BraA.CR.a (Hirani et al., 2018), BraA3P5X.CRa/bKato1.1 (Fredua-Agyeman et al., 2020), Rcr1 (Chu et al., 2014), CRa (Matsumoto et al., 1998), Rcr2 (Huang et al., 2017), BraA3P5X.CRa/bKato1.2 (Fredua-Agyeman et al., 2020), BraA.CR.c (Hirani et al., 2018), CRb (Piao et al., 2004), Rcr4 (Yu et al., 2017), Rcr5 (Huang et al., 2017)]. ...
... Some of the identified CR loci include PbBa1.1 and Crr2 from A01chromosome (Suwabe et al., 2003;Chen et al., 2013), CRc and Rcr8 from A02 chromosome, and the maximum number of 16 from the A03 chromosome [PbBa3.1 (Chen et al., 2013), PbBa3.2 (Chen et al., 2013), Crr3 (Hirai et al., 2004), CRk (Sakamoto et al., 2008), CRd (Pang et al., 2018), PbBa3.3 (Chen et al., 2013), BraA.CR.a (Hirani et al., 2018), BraA3P5X.CRa/bKato1.1 (Fredua-Agyeman et al., 2020), Rcr1 (Chu et al., 2014), CRa (Matsumoto et al., 1998), Rcr2 (Huang et al., 2017), BraA3P5X.CRa/bKato1.2 (Fredua-Agyeman et al., 2020), BraA.CR.c (Hirani et al., 2018), CRb (Piao et al., 2004), Rcr4 (Yu et al., 2017), Rcr5 (Huang et al., 2017)]. In addition, CrrA on A05 and Crr4 on A06 chromosome, and the second number of CR loci on A08 chromosome [PbBa8.1 (Chen et al., 2013), Rcr3 (Karim et al., 2020), Rcr9wa (Karim et al., 2020), BraA.CR.b (Hirani et al., 2018), Rcr9 (Yu et al., 2017), Crr1 (Suwabe et al., 2003), CRs (Laila et al., 2019), CRA8.1 (Wang et al., 2022b)]. ...
The clubroot disease has become a worldwide threat for crucifer crop production, due to its soil-borne nature and difficulty to eradicate completely from contaminated field. In this study we used an elite resistant European fodder turnip ECD04 and investigated its resistance mechanism using transcriptome, sRNA-seq, degradome and gene editing. A total of 1751 DEGs were identified from three time points after infection, among which 7 hub genes including XTH23 for cell wall assembly and two CPK28 genes in PTI pathways. On microRNA, we identified 17 DEMs and predicted 15 miRNA-target pairs (DEM-DEG). We validated two pairs (miR395-APS4 and miR160-ARF) by degradome sequencing. We investigated the miR395-APS4 pair by CRISPR-Cas9 mediated gene editing, the result showed that knocking-out APS4 could lead to elevated clubroot resistance in B. napus. In summary, the data acquired on transcriptional response and microRNA as well as target genes provide future direction especially gene candidates for genetic improvement of clubroot resistance on Brassica species.
... DNA was extracted from resistant and susceptible parents, along with 30 highly resistant (DI = 0; R-pool) and susceptible F 2 plants (DI = 5-7; S-pool) (Supplementary Table 1) following the cetyl trimethyl ammonium bromide method. Bulked segregant analysis (BSA) sequencing (BSA-seq) was performed on four DNA pools (Huang et al., 2017), and sequencing was conducted using the Illumina HiSeq platform, with analysis carried out using NovoGene (http://www.novogene.com). The raw reads underwent quality control trimming to remove low-quality paired reads with the adapter and retained clean reads. ...
Clubroot disease poses a significant threat to Brassica crops, necessitating ongoing updates on resistance gene sources. In F2 segregants of the clubroot-resistant inbred line BrT18-6-4-3 and susceptible DH line Y510, the genetic analysis identified a single dominant gene responsible for clubroot resistance. Through bulk segregant sequencing analysis and kompetitive allele-specific polymerase chain reaction assays, CRA8.1.6 was mapped within 110 kb (12,255–12,365 Mb) between markers L-CR11 and L-CR12 on chromosome A08. We identified B raA08g015220.3.5C as the candidate gene of CRA8.1.6. Upon comparison with the sequence of disease-resistant material BrT18-6-4-3, we found 249 single-nucleotide polymorphisms, seven insertions, six deletions, and a long terminal repeat (LTR) retrotransposon (5,310 bp) at 909 bp of the first intron. However, the LTR retrotransposon was absent in the coding sequence of the susceptible DH line Y510. Given the presence of a non-functional LTR insertion in other materials, it showed that the LTR insertion might not be associated with susceptibility. Sequence alignment analysis revealed that the fourth exon of the susceptible line harbored two deletions and an insertion, resulting in a frameshift mutation at 8,551 bp, leading to translation termination at the leucine-rich repeat domain’s C-terminal in susceptible material. Sequence alignment of the CDS revealed a 99.4% similarity to Crr1a, which indicate that CRA8.1.6 is likely an allele of the Crr1a gene. Two functional markers, CRA08-InDel and CRA08-KASP1, have been developed for marker-assisted selection in CR turnip cultivars. Our findings could facilitate the development of clubroot-resistance turnip cultivars through marker-assisted selection.
... BSR-Seq, an economical and effective approach for gene mapping, is particularly valuable for species with reference genomes. Currently, the BSR-Seq mapping strategy has been widely used to map key genes in Brassica, maize, wheat, and other species [41][42][43][44]. In contrast to traditional methods, BSR-Seq yields comprehensive genetic information, such as SNPs and gene expression data, which greatly accelerates the process of gene mapping. ...
Yellow seed breeding is an effective method to improve oil yield and quality in rapeseed (Brassica napus L.). However, naturally occurring yellow-seeded genotypes have not been identified in B. napus. Mustard (Brassica juncea L.) has some natural, yellow-seeded germplasms, yet the molecular mechanism underlying this trait remains unclear. In this study, a BC9 population derived from the cross of yellow seed mustard “Wuqi” and brown seed mustard “Wugong” was used to analyze the candidate genes controlling the yellow seed color of B. juncea. Subsequently, yellow-seeded (BY) and brown-seeded (BB) bulks were constructed in the BC9 population and subjected to bulked segregant RNA sequencing (BSR-Seq). A total of 511 differentially expressed genes (DEGs) were identified between the brown and yellow seed bulks. Enrichment analysis revealed that these DEGs were involved in the phenylpropanoid biosynthetic process and flavonoid biosynthetic process, including key genes such as 4CL, C4H, LDOX/TT18, PAL1, PAL2, PAL4, TT10, TT12, TT4, TT8, BAN, DFR/TT3, F3H/TT6, TT19, and CHI/TT5. In addition, 111,540 credible single-nucleotide polymorphisms (SNPs) and 86,319 INDELs were obtained and used for quantitative trait locus (QTL) identification. Subsequently, two significant QTLs on chromosome A09, namely, qSCA09-3 and qSCA09-7, were identified by G’ analysis, and five DEGs (BjuA09PAL2, BjuA09TT5, BjuA09TT6, BjuA09TT4, BjuA09TT3) involved in the flavonoid pathway were identified as hub genes based on the protein-to-protein network. Among these five genes, only BjuA09PAL2 and BjuA09F3H had SNPs between BY and BB bulks. Interestingly, the majority of SNPs in BjuA09PAL2 were consistent with the SNPs identified between the high-quality assembled B. juncea reference genome “T84-66” (brown-seed) and “AU213” (yellow-seed). Therefore, BjuA09PAL2, which encodes phenylalanine lyase, was considered as the candidate gene associated with yellow seed color of B. juncea. The identification of a novel gene associated with the yellow seed coloration of B. juncea through this study may play a significant role in enhancing yellow seed breeding in rapeseed.
... Due to the rapid emergence of new pathotypes and the A-genome CR resistance breakdown in 1st generation CR cultivars, it becomes an urgency to utilize polygenic resistance of B. oleracea. Until now, most of the CR genes identified in Canada from A-genome of B. rapa (Yu et al. 2017(Yu et al. , 2016Chu et al. 2014;Huang et al. 2017;Gao et al. 2014;Karim et al. 2020;Rahaman et al. 2022) andB. napus (Fredua-Agyeman et al. 2016;Hasan et al. 2016;Zhang et al. 2016). ...
... alboglabra) assembly ) and the 02-12 (cabbage; B. oleracea var. capitata) assembly ), but their errors and gaps make them difficult to use for many studies (Lee et al. 2016;Liu et al. 2016Liu et al. , 2017Zhang et al. 2015). Another three B. oleracea genomes recently published based on combination of short and long-read technologies; the C-8 (cauliflower; B. oleracea L. var. ...
Key message
Two major quantitative trait loci (QTLs) and five minor QTLs for 10 pathotypes were identified on chromosomes C01, C03, C04 and C08 through genotyping-by-sequencing from Brassica oleracea.
Abstract
Clubroot caused by Plasmodiophora brassicae is an important disease in brassica crops. Managing clubroot disease of canola on the Canadian prairie is challenging due to the continuous emergence of new pathotypes. Brassica oleracea is considered a major source of quantitative resistance to clubroot. Genotyping-by-sequencing (GBS) was performed in the parental lines; T010000DH3 (susceptible), ECD11 (resistant) and 124 BC1 plants. A total of 4769 high-quality polymorphic SNP loci were obtained and distributed on 9 chromosomes of B. oleracea. Evaluation of 124 BC1S1 lines for resistance to 10 pathotypes: 3A, 2B, 5C, 3D, 5G, 3H, 8J, 5K, 5L and 3O of P. brassicae, was carried out. Seven QTLs, 5 originating from ECD11 and 2 from T010000DH3, were detected. One major QTL designated as Rcr_C03-1 on C03 contributed 16.0–65.6% of phenotypic variation explained (PVE) for 8 pathotypes: 2B, 5C, 5G, 3H, 8J, 5K, 5L and 3O. Another major QTL designated as Rcr_C08-1 on C08 contributed 8.3 and 23.5% PVE for resistance to 8J and 5K, respectively. Five minor QTLs designated as Rcr_C01-1, Rcr_C03-2, Rcr_C03-3, Rcr_C04-1 and Rcr_C08-2 were detected on chromosomes C01, C03, C04 and C08 that contributed 8.3–23.5% PVE for 5 pathotypes each of 3A, 2B, 3D, 8J and 5K. There were 1, 10 and 4 genes encoding TIR-NBS-LRR/CC-NBS-LRR class disease resistance proteins in the Rcr_C01-1, Rcr_C03-1 and Rcr_C08-1 flanking regions. The syntenic regions of the two major QTLs Rcr_C03-1 and Rcr_C08-1 in the B. rapa genome ‘Chiifu’ were searched.
... Marker sequences from previously mapped resistance QTL were collected from the literature (Chung et al., 2013;Ferdous et al., 2020;Fujiwara et al., 2011;Hossain et al., 2020;Huang et al., 2017;Jin et al., 2013;Kim et al., 2011Kim et al., , 2013Laila et al., 2019;Long et al., 2011;Matsumoto et al., 2012;Nagaoka et al., 2010;Nguyen et al., 2018;Pang et al., 2018;Saito et al., 2006;Shimizu et al., 2014;Suwabe et al., 2006Suwabe et al., , 2012Yu et al., 2012Yu et al., , 2016Yu et al., , 2017Zhang et al., 2014Zhang et al., , 2018Zhang et al., , 2021 and were BLASTed using Geneious (R6.1.8) to assign the physical location of the QTL in the pangenome. ...
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
... In recent years, many resistance genes to clubroot disease have been located in Chinese cabbage including Crr1, Crr2 (Suwabe et al., 2003), Crr3 (Saito et al., 2006), Crr4 (Suwabe, 2006), CRa (Matsumoto et al., 1998), CRb (Kato et al., 2013), CRc (Sakamoto et al., 2008), CRk (Suwabe et al., 2003), Rcr1 (Chu et al., 2014), Rcr2 (Huang et al., 2017), PbBa3.1, PbBa3.2 (Chen et al., 2013). ...
... For example, Yu et al. (2016) mapped Bra019409 and Bra019410 as candidate genes for the target region of Rcr1 by the combined technology of BSA and KASP. Rcr2 was also fine-located between two SNP sites by the combined technology of BSA and KASP, and finally Bra019410 and Bra019413 were located as the candidate genes of Rcr2 (Huang et al., 2017). In summary, Rcr1 and Rcr2 share a common candidate gene Bra019410. ...
... At present, many R genes to clubroot disease have been mapped in Chinese cabbage. As a common candidate gene for Rcr1 and Rcr2 (Chu et al., 2014;Yu et al., 2016;Huang et al., 2017), Bra019410 was a highly homology protein with RPP1 in Arabidopsis, so it was named BrRPP1. Through the analysis of the conservative domain, we found that the protein contains TIR and LRR and other conservative domains, belonging to TIR-NBS-LRR proteins ( Figure 1A). ...
Introduction
The clubroot disease caused by Plasmodiophora brassicae (P. brassicae) poses a serious threat to the economic value of cruciferous crops, which is a serious problem to be solved worldwide. Some resistance genes to clubroot disease in Brassica rapa L. ssp pekinensis cause by P. brassicae have been located on different chromosomes. Among them, Rcr1 and Rcr2 were mapped to the common candidate gene Bra019410, but its resistance mechanism is not clear yet.
Methods
In this experiment, the differences of BrRPP1 between the resistant and susceptible material of Chinese cabbage were analyzed by gene cloning and qRT-PCR. The gene function was verified by Arabidopsis homologous mutants. The expression site of BrRPP1 gene in cells was analyzed by subcellular localization. Finally, the candidate interaction protein of BrRPP1 was screened by yeast two-hybrid library.
Results
The results showed that the cDNA sequence, upstream promoter sequence and expression level of BrRPP1 were quite different between the resistant and susceptible material. The resistance investigation found that the Arabidopsis mutant rpp1 was more susceptible to clubroot disease than the wild type, which suggested that the deletion of rpp1 reduces resistance of plant to clubroot disease. Subcellular location analysis confirmed that BrRPP1 was located in the nucleus. The interaction proteins of BrRPP1 screened from cDNA Yeast Library by yeast two-hybrid are mainly related to photosynthesis, cell wall modification, jasmonic acid signal transduction and programmed cell death.
Discussion
BrRPP1 gene contains TIR-NBS-LRR domain and belongs to R gene. The cDNA and promoter sequence of BrRPP1 in resistant varieties was different from that in susceptible varieties led to the significant difference of the gene expression of BrRPP1 between the resistant varieties and the susceptible varieties. The high expression of BrRPP1 gene in resistant varieties enhanced the resistance of Chinese cabbage to P. brassicae, and the interaction proteins of BrRPP1 are mainly related to photosynthesis, cell wall modification, jasmonic acid signal transduction and programmed cell death. These results provide important clues for understanding the mechanism of BrRPP1 in the resistance of B. rapa to P. brassicae.
... Matsumoto et al. obtained pure lines with high resistance by mounting three CR genes (CRa, CRk, and CRc), and demonstrated that disease resistance can be elevated by mounting CR genes [95]. By SNP mapping and RNA sequencing, Huang et al. identified two possible CR genes (Bra019410 and Bra019413) from Rcr2 loci in cabbage [96]. Recently, Rsa10003637 and RSA1005569/Rsa10025571 were identified as CR loci from radish; a significant correlation was found between the Rsa10025569 locus and disease resistance in a BC1F1 population [97]. ...
Clubroot disease is a soil-borne disease caused by Plasmodiophora brassicae. It occurs in cruciferous crops exclusively, and causes serious damage to the economic value of cruciferous crops worldwide. Although different measures have been taken to prevent the spread of clubroot disease, the most fundamental and effective way is to explore and use disease-resistance genes to breed resistant varieties. However, the resistance level of plant hosts is influenced both by environment and pathogen race. In this work, we described clubroot disease in terms of discovery and current distribution, life cycle, and race identification systems; in particular, we summarized recent progress on clubroot control methods and breeding practices for resistant cultivars. With the knowledge of these identified resistance loci and R genes, we discussed feasible strategies for disease-resistance breeding in the future.
... genes from different Brassica species involved in P. brassicae resistance (Hasan, Shaikh, et al., 2021;Lv et al., 2020). Due to the lack of CR genes in B. napus (canola, genome AACC) germplasm, the canola progenitor B. rapa (Chinese cabbage, genome AA) is considered as a major source in CR breeding (Huang et al., 2017;Yang et al., 2022). ...
... Several candidate CR genes have been identified to encode NLR proteins in B. rapa (Hatakeyama et al., 2017(Hatakeyama et al., , 2022Huang et al., 2017;Matsumoto et al., 2012;Wang et al., 2022;Yang et al., 2022;Zhang et al., 2021). CRa and Crr1a were successfully iso- RLPs, highlighting the chances to find CR gene members in any of these gene families (Tirnaz et al., 2020). ...
Background:
Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide.
Disease symptoms:
In the advanced stages of clubroot disease wilting, stunting, yellowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club-shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients.
Host range:
Members of the family Brassicaceae are the primary host of the pathogen, although some members of the family, such as Bunias orientalis, Coronopus squamatus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile.
Taxonomy:
Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877).
Distribution:
Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries.
Pathotyping:
Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to understand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 different pathotypes based on the response of a set of 13 hosts.
Effectors and resistance:
After the identification and characterization of the clubroot pathogen SABATH-type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide-binding (NB) site leucine-rich-repeat (LRR) receptors (NLRs) clubroot resistance genes validated to date.
Important link:
Canola Council of Canada is constantly updating information about clubroot and P. brassicae as part of their Canola Encyclopedia: https://www.canolacouncil.org/canola-encyclopedia/diseases/clubroot/.
Phytosanitary categorization:
PLADBR: EPPO A2 list; Annex designation 9E.
... BSR-seq, combining BSA and RNA-seq techniques, has been used in Brassica spp. to determine QTLs, fine mapping and reporting of candidate genes for clubroot resistance encoding TNL resistance proteins [104][105][106][107][108][109]. Using BSR-seq, a major gene, Rcr5 was fine mapped into the 23-31 Mb region of the A3 chromosome, and the identification of several recombinants indicated that Rcr5 was different from the previously mapped clubroot resistance genes (CRa/CRb kato , CRb) on ch. ...
... A3 using BSR-Seq in Chinese cabbage cv. "Jazz" in an interval of 0.4 cM and five SNP markers co-segregating with Rcr2 were identified [105]. In the target region, four genes encoding TNL proteins were detected among which two genes with high numbers of polymorphic variants could be the most likely candidates for Rcr2. ...
... Over the past 20 years, good progress has been made in mapping many promising clubroot-resistant genes/QTLs in the A-genome in B. rapa (Supplementary Table S1). Two resistance loci, CRa and CRb kato are allelic since they are localized in the same position [122], while Rcr1, Rcr2, and Rcr4 were found co-localized with CRa/CRb kato [104,105,111] on A3 chromosome of B. rapa. Additionally, three clubroot resistance hotspots corresponding to Crr3/CRk/CRd and CRa/CRb/CRb kato regions on A3 and Crr1 region on the ch. ...
Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.
... To date, several clubroot resistance loci have been identified on seven of the 10 A genome chromosomes, where a majority of the loci or genes are located on A03 and A08. At least eight loci-CRa/CRb, CRd, CRk, Rcr1, Rcr2, Rcr4, Rcr5, and Crr3-have been reported on A03 (Chu et al., 2014;Hatakeyama et al., 2017;Hirai et al., 2004;Huang et al., 2017Huang et al., , 2019Pang et al., 2018;Piao et al., 2004;Saito et al., 2006;Sakamoto et al., 2008;Ueno et al., 2012;Yu et al., 2016Yu et al., , 2017; for review, see Hasan et al., 2021a), where five of them are located ∼8 Mb downstream of the A03 QTL that we detected in this study, while the loci Crr3, CRk, and CRd are observed to reside in the same genomic region. The flanking or cosegregating markers of Crr3 and CRk were either monomorphic or did not produce any amplification product in our mapping population However, based on search of the BrSTS-78 and BrSTS-33 marker sequences of Crr3 (Hirai et al., 2004;Saito et al., 2006) in the reference genomes v3.1 and v4.1 using the software SnapGene, we could position this locus at 15. Mb of v4.1). ...
Clubroot disease caused by Plasmodiophora brassicae is one of the serious threats to canola (Brassica napus L. subsp. napus) production. The evolution of new pathotypes rendering available resistances ineffective compel the introgression of new resistance into canola and extend our understanding of the genetic and molecular basis of the resistance. In this paper, we report the genetic and molecular basis of clubroot resistance in canola, introgressed from a rutabaga (B. napus L. subsp. rapifera Metzg. ‘Polycross’), by using a doubled‐haploid (DH) mapping population. Whole‐genome resequencing (WGRS)‐based bulked segregant analysis followed by genetic mapping and expression analysis of the genes in resistant and susceptible DH lines at 7 and 14 d after inoculation were carried out. Following this approach, two major quantitative trait loci (QTL) located at 14.41–15.44 Mb of A03 and at 9.96–11.09 Mb of A08 chromosomes and their interaction was observed to confer resistance to pathotypes 3H, 3A, and 3D. Analysis of the genes from the two QTL regions suggested that decreased expression of sugar transporter genes (BnaA03g29290D and BnaA03g29310D) may play an important role in resistance conferred by the A03 QTL, while increased expression of the toll/interleukin‐1 receptor (TIR)–nucleotide binding (NB)–leucine rich repeat (LRR) (TNL) genes (BnaA08g10100D, BnaA08g09220D, and BnaA08g10540D) could be the major determinant of the resistance conferred by the A08 QTL. Single‐nucleotide polymorphism (SNP) allele‐specific polymerase chain reaction (PCR)‐based markers, which could be detected by agarose gel electrophoresis, were also developed from the two QTL regions for use in breeding including pyramiding of multiple clubroot resistance genes.
