Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01

Comparative Analysis of Transcriptomes Reveals Pathways and Verifies Candidate Genes for Clubroot Resistance in Brassica oleracea

Clubroot, a soil-borne disease caused by Plasmodiophora brassicae, is one of the most destructive diseases of Brassica oleracea all over the world. However, the mechanism of clubroot resistance remains unclear. In this research, transcriptome sequencing was conducted on root samples from both resistant (R) and susceptible (S) B. oleracea plants infected by P. brassicae. Then the comparative analysis was carried out between the R and S samples at different time points during the infection stages to reveal clubroot resistance related pathways and candidate genes. Compared with 0 days after inoculation, a total of 4991 differential expressed genes were detected from the S pool, while only 2133 were found from the R pool. Gene function enrichment analysis found that the effector-triggered immunity played a major role in the R pool, while the pathogen-associated molecular pattern triggered immune response was stronger in the S pool. Simultaneously, candidate genes were identified through weighted gene co-expression network analysis, with Bol010786 (CNGC13) and Bol017921 (SD2-5) showing potential for conferring resistance to clubroot. The findings of this research provide valuable insights into the molecular mechanisms underlying clubroot resistance and present new avenues for further research aimed at enhancing the clubroot resistance of B. oleracea through breeding.

Resynthesizing Brassica napus with race specific resistance genes and race non-specific QTLs to multiple races of Plasmodiophora brassicae

Clubroot disease in canola (Brassica napus) continues to spread across the Canadian prairies. Growing resistant cultivars is considered the most economical means of controlling the disease. However, sources of resistance to clubroot in B. napus are very limited. In this study, we conducted interspecific crosses using a B. rapa line (T19) carrying race-specific resistance genes and two B. oleracea lines, ECD11 and JL04, carrying race non-specific QTLs. Employing embryo rescue and conventional breeding methods, we successfully resynthesized a total of eight B. napus lines, with four derived from T19 × ECD11 and four from T19 × JL04. Additionally, four semi-resynthesized lines were developed through crosses with a canola line (DH16516). Testing for resistance to eight significant races of Plasmodiophora brassicae was conducted on seven resynthesized lines and four semi-resynthesized lines. All lines exhibited high resistance to the strains. Confirmation of the presence of clubroot resistance genes/QTLs was performed in the resynthesized lines using SNP markers linked to race-specific genes in T19 and race non-specific QTLs in ECD11. The developed B. napus germplasms containing clubroot resistance are highly valuable for the development of canola cultivars resistant to clubroot.

Comparative transcriptome analysis of canola carrying a single vs stacked resistance genes against clubroot

Pyramiding resistance genes may expand the efficacy and scope of a canola variety against clubroot (Plasmodiophora brassicae), a serious threat to canola production in western Canada. However, the mechanism(s) of multigenic resistance, especially the potential interaction among clubroot resistance (CR) genes, are not well understood. In this study, transcriptome was compared over three canola (Brassica napus L.) inbred/hybrid lines carrying a single CR gene in chromosome A03 (CRaM, Line 16) or A08 (Crr1rutb, Line 20), and both genes (CRaM+Crr1rutb, Line 15) inoculated with a field population (L-G2) of P. brassicae pathotype X, a new variant found in western Canada recently. The line16 was susceptible, while lines 15 and 20 were partially resistant. Functional annotation identified differential expression of genes (DEGs) involved in biosynthetic processes responsive to stress and regulation of cellular process; The Venn diagram showed that the partially resistant lines 15 and 20 shared 1,896 differentially expressed genes relative to the susceptible line 16, and many of these DEGs are involved in defense responses, activation of innate immunity, hormone biosynthesis and programmed cell death. The transcription of genes involved in Pathogen-Associated Molecular Pattern (PAMP)-Triggered and Effector-Triggered Immunity (PTI and ETI) was particularly up-regulated, and the transcription level was higher in line 15 (CRaM + Crr1rutb) than in line 20 (Crr1rutb only) for most of the DEGs. These results indicated that the partial resistance to the pathotype X was likely conferred by the CR gene Crr1rutb for both lines 15 and 20 that functioned via the activation of both PTI and ETI signaling pathways. Additionally, these two CR genes might have synergistic effects against the pathotype X, based on the higher transcription levels of defense-related DEGs expressed by inoculated line 15, highlighting the benefit of gene stacking for improved canola resistance as opposed to a single CR gene alone.

Fine mapping and candidate gene analysis of CRA8.1.6, which confers clubroot resistance in turnip (Brassica rapa ssp. rapa)

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.

RNA-Seq Bulked Segregant Analysis of an Exotic B. napus ssp. napobrassica (Rutabaga) F2 Population Reveals Novel QTLs for Breeding Clubroot-Resistant Canola

In this study, a rutabaga (Brassica napus ssp. napobrassica) donor parent FGRA106, which exhibited broad-spectrum resistance to 17 isolates representing 16 pathotypes of Plasmodiophora brassicae, was used in genetic crosses with the susceptible spring-type canola (B. napus ssp. napus) accession FG769. The F2 plants derived from a clubroot-resistant F1 plant were screened against three P. brassicae isolates representing pathotypes 3A, 3D, and 3H. Chi-square (χ2) goodness-of-fit tests indicated that the F2 plants inherited two major clubroot resistance genes from the CR donor FGRA106. The total RNA from plants resistant (R) and susceptible (S) to each pathotype were pooled and subjected to bulked segregant RNA-sequencing (BSR-Seq). The analysis of gene expression profiles identified 431, 67, and 98 differentially expressed genes (DEGs) between the R and S bulks. The variant calling method indicated a total of 12 (7 major + 5 minor) QTLs across seven chromosomes. The seven major QTLs included: BnaA5P3A.CRX1.1, BnaC1P3H.CRX1.2, and BnaC7P3A.CRX1.1 on chromosomes A05, C01, and C07, respectively; and BnaA8P3D.CRX1.1, BnaA8P3D.RCr91.2/BnaA8P3H.RCr91.2, BnaA8P3H.Crr11.3/BnaA8P3D.Crr11.3, and BnaA8P3D.qBrCR381.4 on chromosome A08. A total of 16 of the DEGs were located in the major QTL regions, 13 of which were on chromosome C07. The molecular data suggested that clubroot resistance in FGRA106 may be controlled by major and minor genes on both the A and C genomes, which are deployed in different combinations to confer resistance to the different isolates. This study provides valuable germplasm for the breeding of clubroot-resistant B. napus cultivars in Western Canada.

A CRISPR/Cas9-based vector system enables the fast breeding of selection-marker-free canola with Rcr1-rendered clubroot resistance

Breeding for disease resistance in major crops is of crucial importance for global food security and sustainability. However, common biotechnologies such as traditional transgenesis or genome editing do not provide an ideal solution, whereas transgenic crops free of selection markers such as cisgenic/intragenic crops might be suitable. In this study, after cloning and functional verification of the Rcr1 gene for resistance to clubroot (Plasmodiophora brassicae), we confirmed that the genes Rcr1, Rcr2, Rcr4, and CRa from Brassica rapa crops and the resistance gene from B. napus oilseed rape cv. 'Mendel' on chromosome A03 were identical in their coding regions. We also determined that Rcr1 has a wide distribution in Brassica breeding materials and renders potent resistance against multiple representative clubroot strains in Canada. We then modified a CRISPR/Cas9-based cisgenic vector system and found that it enabled the fast breeding of selection-marker-free transgenic crops with add-on traits, with selection-marker-free canola (B. napus) germplasms with Rcr1-rendered stable resistance to clubroot disease being successfully developed within 2 years. In the B. napus background, the intragenic vector system was able to remove unwanted residue sequences from the final product with high editing efficiency, and off-target mutations were not detected. Our study demonstrates the potential of applying this breeding strategy to other crops that can be transformed by Agrobacterium. Following the streamlined working procedure, intragenic germplasms can be developed within two generations, which could significantly reduce the breeding time and labor compared to traditional introgression whilst still achieving comparable or even better breeding results.

The effect of phytosulfokine alpha on haploid embryogenesis and gene expression of Brassica napus microspore cultures

Microspore embryogenesis (ME) is the most powerful tool for creating homozygous lines in plant breeding and molecular biology research. It is still based mainly on the reprogramming of microspores by temperature, osmotic and/or nutrient stress. New compounds are being sought that could increase the efficiency of microspore embryogenesis or even induce the formation of haploid embryos from recalcitrant genotypes. Among these, the mitogenic factor phytosulfokine alpha (PSK-α) is promising due to its broad spectrum of activity in vivo and in vitro. The aim of our study was to investigate the effect of PSK-α on haploid embryogenesis from microspores of oilseed rape (Brassica napus L., DH4079), one of the most important oil crops and a model plant for studying the molecular mechanisms controlling embryo formation. We tested different concentrations (0, 0.01, 0.1 and 1 µM) of the peptide and evaluated its effect on microspore viability and embryo regeneration after four weeks of culture. Our results showed a positive correlation between addition of PSK-α and cultured microspore viability and a positive effect also on the number of developed embryos. The analysis of transcriptomes across three time points (day 0, 2 and 4) with or without PSK-α supplementation (15 RNA libraries in total) unveiled differentially expressed genes pivotal in cell division, microspore embryogenesis, and subsequent regeneration. PCA grouped transcriptomes by RNA sampling time, with the first two principal components explaining 56.8% variability. On day 2 with PSK, 45 genes (15 up- and 30 down-regulated) were differentially expressed when PSK-α was added and their number increased to 304 by day 4 (30 up- and 274 down-regulated). PSK, PSKR, and PSI gene expression analysis revealed dynamic patterns, with PSK2 displaying the highest increase and overall expression during microspore culture at days 2 and 4. Despite some variations, only PSK1 showed significant differential expression upon PSK-α addition. Of 16 ME-related molecular markers, 3 and 15 exhibited significant differential expression in PSK-supplemented cultures at days 2 and 4, respectively. Embryo-specific markers predominantly expressed after 4 days of culture, with higher expression in medium without PSK, while on day 0, numerous sporophyte-specific markers were highly expressed.

Identification of QTLs for resistance to 10 pathotypes of Plasmodiophora brassicae in Brassica oleracea cultivar ECD11 through genotyping-by-sequencing

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. 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.

Brassica napus Haploid and Double Haploid Production and Its Latest Applications

Rapeseed is one of the most important oil crops in the world. Increasing demand for oil and limited agronomic capabilities of present-day rapeseed result in the need for rapid development of new, superior cultivars. Double haploid (DH) technology is a fast and convenient approach in plant breeding as well as genetic research. Brassica napus is considered a model species for DH production based on microspore embryogenesis; however, the molecular mechanisms underlying microspore reprogramming are still vague. It is known that morphological changes are accompanied by gene and protein expression patterns, alongside carbohydrate and lipid metabolism. Novel, more efficient methods for DH rapeseed production have been reported. This review covers new findings and advances in Brassica napus DH production as well as the latest reports related to agronomically important traits in molecular studies employing the double haploid rapeseed lines.

Canola with Stacked Genes Shows Moderate Resistance and Resilience against a Field Population of Plasmodiophora brassicae (Clubroot) Pathotype X

Genetic resistance is a cornerstone for managing clubroot (Plasmodiophora brassicae). However, when used repeatedly, a clubroot resistance (CR) gene can be broken rapidly. In this study, canola inbred/hybrid lines carrying one or two CR genes (Rcr1/CRa^M and Crr1^rutb) were assessed against P. brassicae pathotype X by repeated exposure to the same inoculum source under a controlled environment. Lines carrying two CR genes, either Rcr1 + Crr1^rutb or CRa^M + Crr1^rutb, showed partial resistance. Selected lines were inoculated with a field pathotype X population (L-G3) at 5 × 10⁶ resting spores/g soil, and all clubs were returned to the soil they came from six weeks after inoculation. The planting was repeated for five cycles, with diseased roots being returned to the soil after each cycle. The soil inoculum was quantified using qPCR before each planting cycle. All lines with a single CR gene were consistently susceptible, maintaining high soil inoculum levels over time. The lines carrying two CR genes showed much lower clubroot severity, resulting in a 10-fold decline in soil inoculum. These results showed that the CR-gene stacking provided moderate resistance against P. brassicae pathotype X, which may also help reduce the pathogen inoculum buildup in soil.

Identification of a genomic region containing genes involved in resistance to four pathotypes of Plasmodiophora brassicae in Brassica rapa turnip ECD02

Clubroot, caused by Plasmodiophora brassicae, is an important disease of brassica crops worldwide. Vegetable turnip (Brassica rapa L.) have proven to be a source of clubroot resistance genes effective against many pathotypes of P. brassicae. The F₁ progeny from the cross B. rapa canola ACDC (susceptible, S) × B. rapa turnip ECD02 (resistant, R) were backcrossed with ACDC, then self-pollinated to produce BC₁ S₁ lines. All the F₁ plants were resistant to four pathotypes (3A, 3D, 3H, and 5X) of P. brassicae. Segregation for R and S in BC₁ to each pathotype was 1:1 and resistance reactions were highly correlated. From whole genome sequencing, 192.1 M sequences with 96% template coverage from ECD02, and 478.9 M sequences with 92% coverage from ACDC, were aligned with the reference genome of B. rapa. Genotyping-by-sequencing was performed on the BC₁ population. The number of aligned short reads per plant in the BC₁ ranged from 1.4 to 8.5 M sequences with 4-8% template coverage. We obtained 1,344 high-quality single-nucleotide polymorphism (SNP) loci with a mean missing rate at 0.27% and distributed them on 10 chromosomes. A single co-localized quantitative trait loci (QTL), designated as Rcr9^ECD02 on chromosome A08, conferred resistance to the four pathotypes. The QTL explained 68.9-74.4% of phenotypic variation with the logarithm of the odds values of 24.3 to 31.1. Bulked segregant analysis was performed, and 14 SNP markers linked to the gene were developed using the Kompetitive Allele Specific PCR. Rcr9^ECD02 was mapped into an interval of 2.2 cM, flanked by CF_A08_10664692 and CF_A08_12230973, which spanned 1.51 Mb on the chromosome and included 219 B. rapa genes. Four of these genes (BraA08g012910.3C, BraA08g012920.3C, BraA08g013130.3C, and BraA08g013630.3C) encoded disease resistance proteins.

Genetic and molecular analysis reveals that two major loci and their interaction confer clubroot resistance in canola introgressed from rutabaga

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.

Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L

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.