Clubroot resistance QTL are modulated by nitrogen input in <Emphasis Type="Italic">Brassica napus</Emphasis>

Key message

Nitrogen levels can modulate the effectiveness of clubroot resistance in an isolate- and host-specific manner. While the same QTL were detected under high and low nitrogen, their effects were altered.

Abstract

Clubroot, caused by Plasmodiophora brassicae, is one of the most damaging diseases of oilseed rape and is known to be affected by nitrogen fertilization. However, the genetic factors involved in clubroot resistance have not been characterized under nitrogen-limiting conditions. This study aimed to assess the variability of clubroot resistance under different nitrogen levels and to characterize the impact of nitrogen supply on genetic resistance factors. Linkage analyses and a genome-wide association study were conducted to detect QTL for clubroot resistance and evaluate their sensitivity to nitrogen. The clubroot response of a set of 92 diverse oilseed rape accessions and 108 lines derived from a cross between ‘Darmor-bzh’ (resistant) and ‘Yudal’ (susceptible) was studied in the greenhouse under high- and low-nitrogen conditions, following inoculation with the P. brassicae isolates eH and K92-16. Resistance to each isolate was controlled by a major QTL and a few small-effects QTL. While the same QTL were detected under both high and low nitrogen, their effects were altered. Clubroot resistance to isolate eH, but not K92-16, was greater under a low-N supply versus a high-N supply. New sources of resistance were found among the oilseed rape accessions under both low and high-N conditions. The results are discussed relative to the literature and from a crop improvement perspective.

     

Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids

Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26–41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.     

Detection of Genetic Variation in Alternaria brassicae by RAPD Fingerprints

Genetic variation in fourteen isolates of Alternaria brassicae collected from different geographical regions of the world was determined by RAPD (random amplified polymorphic DNA) analysis. Twenty random primers were tried to amplify genomic DNA of A. brassicae. Based on the PCR (polymerase chain reaction) amplification of genomic DNA of A. brassicae with four oligonucleotide random primers, fingerprints were generated for each isolate and the amplifed products were compared. Using this technique, intra- and intercontinental genetic variation among isolates of A. brassicae could be distinguished.     

A Possible Proteome-level Explanation for Differences in Virulence of Two Isolates of a Fungal Pathogen Alternaria brassicae

Brassica napus (canola) is an important oilseed crop in many countries throughout the world including Canada. One of the major constraints on canola productivity is blackspot disease caused by the necrotrophic phytopathogenic fungus Alternaria brassicae. Two isolates of A. brassicae with significant differences in virulence have been characterized at the proteomelevel. The morphological observations indicated the Ontario isolate to be more virulent by virtue of increased disease severity score as compared to the UAMH7476 isolate. This was further confirmed through histological observations that indicated extensive colonization of the host tissue by the highly virulent isolate. Mycelial protein profiles of two differentially virulent A. brassicae isolates were compared using two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) in order to identify proteins that may be responsible for the observed differences. The investigation suggested several differences in the mycelial proteomes of the two isolates. The proteins that were significantly abundant in the more virulent isolate included a protein with conserved actin related protein 2/3 domain, enolase, malate dehydrogenase and serine protease. These results suggest that the differential protein expression pattern could be exploited to identify putative virulence and pathogenicity factors in A. brassicae.     

Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa

Clubroot disease is one of the major diseases affecting Brassicaceae crops, and a number of these crops grown commercially, such as Chinese cabbage (Brassica rapa L. ssp. pekinensis), are known to be highly susceptible to clubroot disease. To provide protection from this disease, plant breeders have introduced genes for resistance to clubroot from the European turnip into susceptible lines. The CRa gene confers specific resistance to the clubroot pathogen Plasmodiophora brassicae isolate M85. Fine mapping of the CRa locus using synteny to the Arabidopsis thaliana genome and partial genome sequences of B. rapa revealed a candidate gene encoding a TIR-NBS-LRR protein. Several structural differences in this candidate gene were found between susceptible and resistant lines, and CRa expression was observed only in the resistant line. Four mutant lines lacking clubroot resistance were obtained by the UV irradiation of pollen from a resistant line, and all of these mutant lines carried independent mutations in the candidate TIR-NBS-LRR gene. This genetic and molecular evidence strongly suggests that the identified gene is CRa. This is the first report on the molecular characterization of a clubroot Resistance gene in Brassicaceae and of the disease resistance gene in B. rapa.     

Status and Perspectives of Clubroot Resistance Breeding in Crucifer Crops

Clubroot disease is a major threat to crops belonging to the Brassicaceae. It is controlled most effectively by the use of resistant cultivars. Plasmodiophora brassicae, the causal agent, shows a wide variation for pathogenicity, which can be displayed by using differential host sets. Except for Brassica juncea and B. carinata, resistant accessions can be found in all major crops. Most resistance sources are race-specific, despite some race-independent resistant accessions which can be found in B. oleracea. European field isolates from P. brassicae display great variation and show a tendency to overcome different resistance sources from either B. rapa or B. oleracea. At present, resistance genes from stubble turnips (B. rapa) are most effective and most widely used in resistance breeding of different Brassica crops. Resistance to P. brassicae from turnips was introduced into Chinese cabbage, oilseed rape, and B. oleracea. Although most turnips carry more than one resistance gene, the resistant cultivars from other crops received primarily a single, dominant resistance gene having a race-specific effect. Populations of P. brassicae that are compatible against most of the used resistance sources have been present in certain European areas for many decades. Such pathogen populations appeared in Japanese Chinese cabbage crops only a few years after the introduction of resistant cultivars. As the spread of virulent P. brassicae pathotypes seems to be slow, resistant cultivars are still a very effective method of control in many cropping areas. Mapping studies have revealed the presence of several clubroot-resistance genes in the Brassica A and C genomes; most of these genes are showing race specificity. Only in B. oleracea was one broad-spectrum locus detected. Two loci from the A genome confer resistance to more than one pathotype, but not to all isolates. Progress made in the determination of resistance loci should be used to formulate and introduce an improved differential set. Future efforts for breeding P. brassicae resistance will focus on durability by broadening the genetic basis of clubroot resistance by using either natural variation or transgenic strategies.     

The comparative susceptibilities of Pieris brassicae and P. rapae to a granulosis virus from P. brassicae

A comparison was made of the dosage-mortality responses of larvae of Pieris brassicae and P. rapae to infection by P. brassicae granulosis virus (GV). Bioassays with first, second, third, and fourth-instar larvae of both species revealed a marked difference in susceptibility between instars and between species. Median lethal dosages (LD₅₀s) for P. rapae larvae ranged from five capsules for the first instar to 662 capsules for the fourth instar. With P. brassicae, this range extended from 66 capsules to 2.3 × 10⁷ capsules. The time-mortality responses of the two species were similar when fed virus dosages equivalent to an LD₉₀. Median lethal times (LT₅₀s) ranged from 5 days for first-instar larvae to 7–8 days for fourth-instar larvae. A comparison between a long-established laboratory stock of P. brassicae and a stock recently acquired from the field showed no significant difference in their susceptibility to GV. The implications of the pronounced species differences in susceptibility to GV infection are discussed in relation to the potential field control of P. rapae and P. brassicae.     

Preliminary observations on variation in susceptibility to clubroot among collections of some wild crucifers

Collections of Capsella bursa-pastoris and other common cruciferous weeds showed significant differences in susceptibility to populations of Plasmodiophora brassicae as defined on the European Clubroot Differential (ECD) set. Some evidence was obtained that selection for tolerance may occur within natural populations of C. bursa-pastoris. Overall virulence of P. brassicae collections on the ECD set was not correlated with virulence to the weeds tested. The significance of wild hosts in studies of resistance to P. brassicae is discussed.     

Morphological and molecular characterizations of the Gregarina sp. (Apicomplexa: Protozoa) parasitizing on Phaedon brassicae (Coleoptera: Chrysomelidae)

A gregarine parasite (Eugregarinida: Gregarinidae) was observed in the population of daikon leaf beetle, Phaedon brassicae Baly, (Coleoptera: Chrysomelidae) in Korea. Gregarines are well known species-specific parasites of various Arthropoda. This Gregarina sp. also confirmed a species-specific parasite in P. brassicae. Based on 1.727 kb of 18S rDNA sequence (FJ481523), this gregarine species was grouped in eugregarine and a 5.258 kb of full length rDNA replicon was cloned (JF412715). We also observed interaction of trophozoite or gamonto of gregarine and epithelium of a host midgut using a light microscope and a scanning electron microscope. Although the developmental period of the infected host is delayed half a day in every larval stage, there was no significant difference in the developmental period of P. brassicae whether Gregarina sp. was infected or not. Gregarina sp. was a kind of facultative parasite from P. brassicae. This is the first report of a gregarine parasite in P. brassicae.     

De novo Genome Assembly of the Fungal Plant Pathogen Pyrenophora semeniperda

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species.     

Role of Proteolysis in Determining Potency of Bacillus thuringiensis Cry1Ac δ-Endotoxin

Bacillus thuringiensis protein δ-endotoxins are toxic to a variety of different insect species. Larvicidal potency depends on the completion of a number of steps in the mode of action of the toxin. Here, we investigated the role of proteolytic processing in determining the potency of the B. thuringiensis Cry1Ac δ-endotoxin towards Pieris brassicae (family: Pieridae) and Mamestra brassicae (family: Noctuidae). In bioassays, Cry1Ac was over 2,000 times more active against P. brassicae than against M. brassicae larvae. Using gut juice purified from both insects, we processed Cry1Ac to soluble forms that had the same N terminus and the same apparent molecular weight. However, extended proteolysis of Cry1Ac in vitro with proteases from both insects resulted in the formation of an insoluble aggregate. With proteases from P. brassicae, the Cry1Ac-susceptible insect, Cry1Ac was processed to an insoluble product with a molecular mass of ~56 kDa, whereas proteases from M. brassicae, the non-susceptible insect, generated products with molecular masses of ~58, ~40, and ~20 kDa. N-terminal sequencing of the insoluble products revealed that both insects cleaved Cry1Ac within domain I, but M. brassicae proteases also cleaved the toxin at Arg423 in domain II. A similar pattern of processing was observed in vivo. When Arg423 was replaced with Gln or Ser, the resulting mutant toxins resisted degradation by M. brassicae proteases. However, this mutation had little effect on toxicity to M. brassicae. Differential processing of membrane-bound Cry1Ac was also observed in qualitative binding experiments performed with brush border membrane vesicles from the two insects and in midguts isolated from toxin-treated insects.     

Draft Genome Sequence of the Pseudomonas aeruginosa Bloodstream Isolate PABL056

Pseudomonas aeruginosa is an important cause of disease in hospitalized and immunocompromised patients. The genome of P. aeruginosa is among the largest of bacteria pathogenic to humans. We present the draft genome sequence of P. aeruginosa strain PABL056, a human bloodstream isolate with the largest genome yet reported in P. aeruginosa.     

A tritrophic approach to the preference–performance hypothesis involving an exotic and a native plant

Exotic plants often generate physical and chemical changes in native plant communities where they become established. A major challenge is to understand how novel plants may affect trophic interactions in their new habitats, and how native herbivores and their natural enemies might respond to them. We compared the oviposition preference and offspring performance of the crucifer specialist, Pieris brassicae, on an exotic plant, Bunias orientalis, and on a related native plant, Sinapis arvensis. Additionally, we studied the response of the parasitoid, Cotesia glomerata to herbivore-induced plant volatiles (HIPV) and determined the volatile blend composition to elucidate which compound(s) might be involved in parasitoid attraction. On both host plants we also compared the parasitism rate of P. brassicae by C. glomerata. Female butterflies preferred to oviposit on the native plant and their offspring survival and performance was higher on the native plant compared to the exotic. Although, headspace analysis revealed qualitative and quantitative differences in the volatile blends of both plant species, C. glomerata did not discriminate between the HIPV blends in flight-tent bioassays. Nevertheless, parasitism rate of P. brassicae larvae was higher on the native plant under semi-field conditions. Overall, P. brassicae oviposition preference may be more influenced by bottom-up effects of the host plant on larval performance than by top-down pressure exerted by its parasitoid. The potential for dietary breadth expansion of P. brassicae to include the exotic B. orientalis and the role of top-down processes played by parasitoids in shaping herbivore host shifts are further discussed.     

Ecological fits, mis-fits and lotteries involving insect herbivores on the invasive plant, Bunias orientalis

Exotic plants bring with them traits that evolved elsewhere into their new ranges. These traits may make them unattractive or even toxic to native herbivores, or vice versa. Here, interactions between two species of specialist (Pieris rapae and P. brassicae) and two species of generalist (Spodoptera exigua and Mamestra brassicae) insect herbivores were examined on two native crucifer species in the Netherlands, Brassica nigra and Sinapis arvensis, and an exotic, Bunias orientalis. Bu. orientalis originates in eastern Europe and western Asia but is now an invasive pest in many countries in central Europe. P. rapae, P. brassicae and S. exigua performed very poorly on Bu. orientalis, with close to 100% of larvae failing to pupate, whereas survival was much higher on the native plants. In choice experiments, the pierid butterflies preferred to oviposit on the native plants. Alternatively, M. brassicae developed very poorly on the native plants but thrived on Bu. orientalis. Further assays with a German Bu. orientalis population also showed that several specialist and generalist herbivores performed very poorly on this plant, with the exception of Spodoptera littoralis and M. brassicae. Bu. orientalis produced higher levels of secondary plant compounds (glucosinolates) than B. nigra but not S. arvensis but these do not appear to be important factors for herbivore development. Our results suggest that Bu. orientalis is a potential demographic ‘trap’ for some herbivores, such as pierid butterflies. However, through the effects of an evolutionary ‘lottery’, M. brassicae has found its way through the plant’s chemical ‘minefield’.     

Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)

Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F₂ individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F_{2 : 3} progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02–12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02–12 genome sequence.     

Whole Mitochondrial Genome Sequence of an Indian Plasmodium falciparum Field Isolate

Mitochondrial genome sequence of malaria parasites has served as a potential marker for inferring evolutionary history of the Plasmodium genus. In Plasmodium falciparum, the mitochondrial genome sequences from around the globe have provided important evolutionary understanding, but no Indian sequence has yet been utilized. We have sequenced the whole mitochondrial genome of a single P. falciparum field isolate from India using novel primers and compared with the 3D7 reference sequence and 1 previously reported Indian sequence. While the 2 Indian sequences were highly divergent from each other, the presently sequenced isolate was highly similar to the reference 3D7 strain.     

Some allelochemicals of Pteridium aquilinum and their involvement in resistance to Pieris brassicae

A number of polar and semi-polar compounds from bracken, Pteridium aquilinum L. Kühn, were screened for feeding deterrent activity to Pieris brassicae L. At natural concentrations, 2 out of 4 flavonoids tested were stimulatory and one was inhibitory; while 2 out of 4 benzoic, and 4 out of 5 cinnamic acid derivatives were inhibitory. Prunasin and its enzymatic hydrolysates had no effect on feeding. It was concluded that braken flavonoids and cyanogenic glycoside were unlikely to be involved in resistance of polar bracken extracts to P. brassicae, while benzoic and cinnamic acids and condensed tannins were probably involved. A number of other benzoic and cinnamic acid derivatives not occurring in bracken were screened, and distinct relationships between chemical structure and feeding deterrent activity to P. brassicae were demonstrated.