Blackleg disease, caused by the ascomycete fungal pathogen Leptosphaeria maculans, is a devastating disease of canola (Brassica napus) in Australia, Canada and Europe. The pathogen is considered a global invasive species and poses a threat to canola production in China, where only the weakly aggressive strain L. biglobosa is present. In Canada, breakdown of blackleg resistance has been shown. In order to develop a more effective disease management strategy, there is a need to elucidate host resistance and defense mechanisms underlying the B. napus-L. maculans pathosystem. This is the very first study to investigate major resistance genes (R genes) and adult plant resistance (APR) in Canadian canola germplasm. This study also analyzed the avirulence allele frequency in L. maculans populations in western Canada. R genes were detected in the majority of these B. napus germplasm, with the Rlm3 gene being predominant. The frequency of AvrLm3 allele in field fungal populations was extremely low. APR was identified in more than 50% of the germplasm. This indicated the breakdown of Rlm3 resistance, which could be due to the widespread use of this single resistance gene in Canadian B. napus germplasm and varieties. To address concerns of introducing L. maculans from Canada into China, this study further characterized R genes and APR to L. maculans in a collection of Chinese B. napus germplasm. R genes were detected in more than 40% of the germplasm tested, with Rlm3 and Rlm4 being predominant. A large portion of the Chinese germplasm showed high to moderate ii APR in field trials at three locations in MB, SK and AB in western Canada. This study highlighted the availability of fair to good resistance in the Chinese B. napus germplasm against blackleg disease and was the first study to investigate a large number of Chinese germplasm against Canadian fungal populations in different environments. RNA sequencing of resistant and susceptible host tissues and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L. maculans LepR1-AvrLepR1 interaction. The sequencing data coupled with functional characterization of some unique genes, in depth histological analysis, and in situ gene activity analysis directly at the site of infection provide unprecedented spatial and temporal resolution of the plant defense response to L. maculans.

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

No abstract

Blackleg, caused by Leptosphaeria maculans, is one of the most economically important diseases of Brassica napus worldwide. Two blackleg-resistant lines, 16S and 61446, were developed through interspecific hybridization between B. napus and B. rapa subsp. sylvestris and backcrossing to B. napus. Classical genetic analysis demonstrated that a single recessive gene in both lines conferred resistance to L. maculans and that the resistance alleles were allelic. Using BC(1) progeny derived from each resistant plant, this locus was mapped to B. napus linkage group N6 and was flanked by microsatellite markers sN2189b and sORH72a in an interval of about 10 cM, in a region equivalent to about 6 Mb of B. rapa DNA sequence. This new resistance gene locus was designated as LepR4. The two lines were evaluated for resistance to a wide range of L. maculans isolates using cotyledon inoculation tests under controlled environment conditions, and for stem canker resistance in blackleg field nurseries. Results indicated that line 16S, carrying LepR4a, was highly resistant to all isolates tested on cotyledons and had a high level of stem canker resistance under field conditions. Line 61446, carrying LepR4b, was only resistant to some of the isolates tested on cotyledons and was weakly resistant to stem canker under field conditions.

Leptosphaeria maculans is the causal agent of blackleg, a serious disease on canola/rapeseed in western Canada, Australia and Europe. Genetic resistance and extended crop rotation provided effective disease control in western Canada for years but the emergence of new pathogen races has reduced the effectiveness of current management strategies. The objective of this study was to analyse L. maculans isolates derived from canola stubble in commercial fields collected in 2010 and 2011 across western Canada for the presence and frequency of avirulence (Avr) genes. A total of 674 isolates were examined for the presence of Avr alleles AvrLm1, AvrLm2, AvrLm3, AvrLm4, AvrLm6, AvrLm7, AvrLm9, AvrLepR1, AvrLepR2 and AvrLmS using a set of differential host genotypes carrying known resistance genes or PCR amplification of AvrLm1, AvrLm6 and AvrLm4-Lm7. Certain alleles were more prevalent in the pathogen population, with AvrLm6 and AvrLm7 present in >85% of isolates, while AvrLm3, AvrLm9 and AvrLepR2 were present in <10% of isolates. A total of 55 races (different combinations of Avr alleles) were detected, with the two most common ones being AvrLm2-Lm4-Lm6-Lm7 and AvrLm2-Lm4-Lm6-Lm7-LmS. Races carrying as many as seven and as few as one known Avr allele were detected. Selection pressure from the race-specific resistance genes carried in canola cultivars has probably played a significant role in the current Avr profile, which may have also contributed to the recent increase in blackleg observed in western Canada.