BackgroundThe protist Plasmodiophora brassicae is a biotrophic soil-borne pathogen that causes clubroot on Brassica crops worldwide. Clubroot disease is a serious threat to the 8 M ha of canola (Brassica napus) grown annually in western Canada. While host resistance is the key to clubroot management, sources of resistance are limited.ResultsTo identify new sources of clubroot resistance (CR), we fine mapped a CR gene (Rcr1) from B. rapa ssp. chinensis to the region between 24.26 Mb and 24.50 Mb on the linkage group A03, with several closely linked markers identified. Transcriptome analysis was conducted using RNA sequencing on a segregating F1 population inoculated with P. brassicae, with 2,212 differentially expressed genes (DEGs) identified between plants carrying and not carrying Rcr1. Functional annotation of these DEGs showed that several defense-related biological processes, including signaling and metabolism of jasmonate and ethylene, defensive deposition of callose and biosynthesis of indole-containing compounds, were up-regulated significantly in plants carrying Rcr1 while genes involved in salicylic acid metabolic and signaling pathways were generally not elevated. Several DEGs involved in metabolism potentially related to clubroot symptom development, including auxin biosynthesis and cell growth/development, showed significantly lower expression in plants carrying Rcr1.ConclusionThe CR gene Rcr1 and closely linked markers will be highly useful for breeding new resistant canola cultivars. The identification of DEGs between inoculated plants carrying and not carrying Rcr1 is an important step towards understanding of specific metabolic/signaling pathways in clubroot resistance mediated by Rcr1. This information may help judicious use of CR genes with complementary resistance mechanisms for durable clubroot resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1166) contains supplementary material, which is available to authorized users.

Renewed interest in Camelina sativa is primarily due to the unique fatty acid profile of the seed oil and its potential value in industry, cosmetics and human nutrition. To exploit C. sativa in western Canada, more information is needed on the performance of this crop in this region. Following a preliminary evaluation in 2001, replicated agronomic trials were conducted in 2002 and 2005 with 19 C. sativa and three oilseed Brassica accessions at Saskatoon and Scott, Saskatchewan and Beaverlodge, Alberta. The C. sativa accessions matured relatively early and were more tolerant of drought and flea beetle infestations than the Brassica oilseeds. Some C. sativa accessions had seed yields competitive with those of the Brassica oilseeds, but seed size was significantly smaller. Seed yields and oil contents of all crop species tested were highest at Beaverlodge, the most northern location. The Brassica oilseeds generally had higher oil contents than C. sativa; the highest oil contents of each crop species tested were associated with the lowest protein contents. In general, average oil and protein contents for C. sativa ranged from 38 to 43% and from 27 to 32%, respectively; for the Brassica checks, oil and protein contents ranged from 38 to 53% and from 21 to 33%, respectively, across all species. Variation in fatty acid composition was higher among the C. sativa accessions than among locations, but overall the ranges of individual fatty acids were relatively narrow. The most abundant fatty acids were oleic (12.8–14.7%), linoleic (16.3–17.2%), linolenic (36.2–39.4%) and eicosenoic (14.0–15.5%). The prospects of developing improved C. sativa germplasm for particular western Canadian environments are good; of primary importance are increased seed size and oil content. Additionally, stand establishment, fertility requirements and broadleaf weed control options need to be investigated. Acceptance of this species as a new oilseed crop for western Canada will also require developing sustainable markets for the oil and meal. Key words: Camelina sativa, seed quality, agronomic trait, oil and protein content, fatty acid

Clubroot, caused by Plasmodiophora brassicae, is an important disease of Brassica crops worldwide. F1 progeny from the Brassica rapa lines T19 (resistant) × ACDC (susceptible) were backcrossed with ACDC, then self-pollinated to produce BC1S1 lines, From genotyping-by-sequencing (GBS) of the parental lines and BC1 plants, about 1.32 M sequences from T19 were aligned into the reference genome of B. rapa with 0.4-fold coverage, and 1.77 M sequences with 0.5-fold coverage in ACDC. The number of aligned short reads per plant in the BC1 ranged from 0.07 to 1.41 M sequences with 0.1-fold coverage. A total of 1584 high quality SNP loci were obtained, distributed on 10 chromosomes. A single co-localized QTL, designated as Rcr4 on chromosome A03, conferred resistance to pathotypes 2, 3, 5, 6 and 8. The peak was at SNP locus A03_23710236, where LOD values were 30.3 to 38.8, with phenotypic variation explained (PVE) of 85–95%. Two QTLs for resistance to a novel P. brassicae pathotype 5x, designated Rcr8 on chromosome A02 and Rcr9 on A08, were detected with 15.0 LOD and 15.8 LOD, and PVE of 36% and 39%, respectively. Bulked segregant analysis was performed to examine TIR-NBS-LRR proteins in the regions harboring the QTL.

Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar “Flower Nabana”. In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.

Information on genetic diversity and genetic relationships among genotypes of Brassica carinata is currently limited. The objectives of this study were to evaluate patterns and levels of genetic diversity in B. carinata based on amplified fragment length polymorphisms (AFLP) as compared with Brassica juncea and Brassica nigra, and to evaluate agronomic and seed quality data for plants grown in the field in western Canada. A total of 296 AFLP bands were generated from four primer pair combinations and scored for presence/ absence in 66, 20 and 7 accessions of B. carinata, B. juncea and B. nigra, respectively. B. carinata was less genetically diverse than the other two species. Differences in diversity were evident in the proportion of polymorphic loci within each species: 23, 35 and 50% for B. carinata, B. nigra and B. juncea, respectively. Pair-wise similarity measures based on the Jaccard coefficient were highest among accessions of B. carinata and showed the narrowest range: 0.911 (0.810-0.981) compared to B. nigra: 0.569 (0.438-0.660) and B. juncea: 0.715 (0.345-0.951). AFLP-based genetic distance information can be used by plant breeders to select diverse genotypes. AFLPs are also useful for fingerprinting cultivars and two primer pair combinations were sufficient to uniquely identify all the accessions of B. carinata. More variation among accessions was identified in the agronomic trial than had previously been described in studies of B. carinata in western Canada, but the data were too limited to draw conclusions regarding specific accessions. Overall, the findings were in agreement with other published work describing the favourable agronomic potential of this species.