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Overcoming blackleg disease

Designing canola cultivars with multigenic durable resistance to blackleg disease.

June 3, 2024  By Donna Fleury

Growth chamber based screening for adult plant resistance against blackleg disease. Image courtesy of Dr. P. Haddadi, AAFC-Saskatoon

Canola growers rely on cultivars with genetic resistance as the best practice for managing blackleg disease, as fungicides have little effect in controlling blackleg. However, recently, the risk of blackleg incidence and severity is increasing, with the breakdown of the current resistance observed in some cultivars caused by the emergence of new virulent isolates.

Repeated use of the same resistance gene leads to the selection of virulent isolates of the blackleg pathogen Leptosphaeria maculans. Tighter rotations shorter than two or three years between canola crops in areas of high infection can also increase the risk. Continuing to develop cultivars with more durable resistance is a priority for researchers and canola breeders. 

“We recently completed a five-year project focused on quantitative resistance (QR), also called adult plant resistance (APR), to control L. maculans in canola,” says Hossein Borhan, research scientist, molecular plant pathology with Agriculture and Agri-Food Canada (AAFC) in Saskatoon. “Two types of resistance, qualitative resistance conferred by race-specific R genes, and quantitative resistance (QR) conferred by non-race-specific genes (QTL), can be used to manage this disease in commercial cultivars. APR is the most favourable form of genetic resistance because it is multigenic and provides resistance that is effective against many pathogen isolates, making the resistance more durable. However, APR is more difficult to work with for researchers and plant breeders because, unlike race-specific disease evaluation that is conducted indoors, APR tests are carried out in the field under unpredictable and less controlled conditions. Typically, QR gene identification is conducted in field trials, which requires several years of testing before having reliable results. It is also more challenging to identify and introduce APR into a breeding program.”


Borhan set out to address those challenges in his lab to optimize a standard screening protocol for identifying APR to blackleg disease under controlled conditions and to validate the result under field conditions. A rapid screening method would provide the canola industry with a valuable tool for developing new APR varieties. Other objectives were to map major QTL genes, identify the causative genes and develop markers specific to those QTL genes.

“We developed a growth chamber-based screening test for an APR assay, mimicking the natural infection cycle that occurs in the field,” Borhan explains. “The canola seedlings were inoculated with highly virulent L. maculans isolates, which is what occurs naturally in the field. The pathogen was allowed to grow into the stem similar to field infection. Blackleg disease was evaluated by measuring the size of the stem canker formed at the base of the stem at eight to 12 weeks after the initial infection. This whole indoor process takes about two-and-a-half to three months, and we can typically complete three or four rounds of screening and have reliable results within one year. In comparison, field screening requires four or five years of testing, which may or may not work because of environmental or other factors that could compromise a field experiment.”

An indoor test of a susceptible (S) canola (Brassica napus) line and a line with quantitative (QTL) resistance against the blackleg pathogen Leptosphaeria maculans. Seedlings were inoculated with a virulent isolate of L. maculans. Plants were kept in a growth chamber and assessed at 12 weeks post-inoculation.

In the second part of the project, using a well-defined and field-tested Brassica napus population, researchers combined mapping and gene expression data to identify several candidate QTLs with a high probability of controlling the APR response.

“We screened about 200 B. napus lines and confirmed 40 lines with major QTL resistance, which had already been previously identified in the field,” Borhan notes. “We tested the QTL resistance genes in those 40 lines using markers that had been developed, and the results correlated very well with the assay screening. We then shared these QTLs with colleagues in Alberta to test in the field. The trial results showed that many of those QTLs were effective when infected with a mixture of L. maculans pathogen isolates and showed a good level of blackleg resistance in the field. A major QTL based on the growth chamber test was identified, which was the same as a major QTL identified in the field, proving the reliability of the indoor APR test to quickly provide growers with effective and durable QTL resistance to blackleg disease.”

The QTL screening and field testing also identified for the first time one of the significant causative QTL resistance genes. This new QTL gene discovery is an important first step in understanding the molecular mechanism of QTL resistance. QTL gene-specific markers will allow breeders to accurately introduce quantitative resistance against blackleg into commercial varieties. Additional research is currently underway to further test this gene in transgenic susceptible backgrounds to understand how these genes behave in different susceptible genotypes.

Other next steps are to determine how common the major QTL resistance genes identified in this project are in other QTL germplasms and how effective they are in conferring resistance against multiple races of the blackleg pathogen in different locations.

“As a result of the project, we were successful in optimizing and proving the reliability of the indoor QTL screening assay and its correlation with the field QTLs,” Borhan says. “This high-throughput screening will enable breeders to identify canola varieties with quantitative resistance to blackleg disease and incorporate QR genes into breeding programs faster and more accurately. The QTL resistance genes can also be combined with major single-race resistance genes to provide a more durable and effective type of resistance for farmers.”

Borhan adds that going forward, his lab and other researchers will continue to investigate how to successfully apply the outcome of this research in designing canola cultivars with durable resistance to blackleg.

“Blackleg research has significantly advanced in the past two decades. We have provided the canola industry with 12 race-specific resistance genes against blackleg and molecular markers for rapid determination of blackleg races in the field. Our understanding of quantitative resistance against blackleg has also advanced considerably; however, further research is needed to identify major QTL genes that are commonly present in various germplasms.” 

“The good news for farmers is they should be able to continue to effectively control blackleg with genetic resistant varieties and by determining the race structure of blackleg in their field to use the best resistance genes against the most prevalent races in their field. Blackleg research achievements are one of the best examples of how the support farmers have provided through their grower association funding has paid back. The blackleg research efforts by AAFC researchers and canola breeders, together with collaborating industry partners, are a great example of how research investments really help farmers successfully address significant disease issues in their cropping systems.” 


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