High-throughput genotyping—a game-changer for agricultural screening
Quality control in agriculture is critical for ensuring that food products are safe and include desirable properties. One of the most widely cultivated crops in the world is wheat, with Canada as one of the world’s largest producers, generating 35 million tons of grain annually. Canadian wheat is comprised of over 500 registered varieties that can be subdivided into over 15 different classes. Of these varieties, certain types of wheat might perform differently based on local climate, soil conditions, and farm management practices. Moreover, the identification of pests, microbial pathogens, and fungal diseases is critical for maintaining quality and optimizing yield. Consequently, tools that allow for high-throughput identification of wheat variety profiles and diseases are required for efficient and accurate quality control.
Rapid identification of crop varieties with higher call rates
With improvements in DNA testing technology, high-throughput genotyping by qPCR (HT-qPCR) has emerged as an ideal tool for agricultural applications. Indeed, detection of single nucleotide polymorphisms (SNPs) with HT-qPCR has seen considerable utility in crop variety identification and high-throughput characterization of numerous wheat varieties.
Lee and colleagues from the Canadian Grain Commission compared the accuracy and throughput of HT-qPCR platforms (see Table 1), including the Takara Bio SmartChip system. Following generation of a validated panel of 32 SNP markers for wheat varieties, DNA samples from seeds were processed with HT-qPCR using either the OpenArray platform (ThermoFisher) or Takara Bio SmartChip System. The researchers found that both systems provide high-throughput and cost-effective processing, along with excellent compatibility between the OpenArray and SmartChip systems. Interestingly, analyses of the 32-marker panel with the SmartChip system resulted in more accurate genotyping calls than the OpenArray platform. This included fewer “no-calls” and successful genotype calls with the SmartChip system that OpenArray missed. Of note, OpenArray failed to identify four critical markers for distinguishing wheat varieties while SmartChip was successful in calling the varieties correctly. The authors further emphasize that the SmartChip system’s 36 markers x 144 sample format allows for additional assays for similar marker patterns that require additional assays.
Improved detection of fungal diseases with HT-qPCR
Image: Wheat displaying Fusarium head blight symptoms
The most prevalent fungal disease found in wheat grain is Fusarium head blight (FHB), caused by fungi in the Fusarium genus, and can lead to severe loss in yield and mycotoxin contamination. Similar to wheat variety identification, application of HT-qPCR for monitoring FHB has also bolstered quality control efficiency and throughput.
Symptoms of fungal disease on wheat plants can be easy to identify but causes can arise from multiple species of fusarium. In North America, the predominant species that causes FHB is F. graminearum, which can be classified by two genotypes based on their ability to form trichothecene derivatives (naturally occurring poisons produced by fungi), acetyldeoxynivalenol (15-ADON) and 3-acetyldeoxynivalenol (3-ADON). Considering the heterogeneity found in fungal diseases in wheat, Bamforth and colleagues from the Canadian Grain Commission expanded their efforts in characterizing FHB from microscopic examinations to HT-qPCR for tricothecene genotypes.
These researchers tested 55,444 wheat kernels from across Canada between 2014 to 2020 using the Takara Bio SmartChip system. In addition to detecting F. graminearum in a majority of fusarium damaged kernels (FDKs), there was also significant variability in levels of other fusarium species. This diversity was attributed to differences in geographical location, overall health of host plants, environmental differences, and on-farm disease management practices. This heterogeneity can also be observed in FDKs that expressed the 15-ADON or 3-ADON genotypes where proportions of FDKs with either genotype varied depending on geographical location. Notably, the incidence of FDKs with the 15-ADON genotype has decreased over the last decade in eastern Canada, while there was a corresponding increase in the more aggressive 3-ADON genotype.
High-throughput, accurate SNP genotyping improves wheat quality control
- The Takara Bio SmartChip system provides a high-throughput platform for detecting SNPs in numerous wheat varieties with high accuracy and improved call rates compared to other platforms.
- Utilization of HT-qPCR with the SmartChip system revealed important insight into the heterogeneity of the leading cause of crop yield loss, Fusarium head blight (FHB). These data allow for improved quality control protocols that can be tailored based on geographical location, environmental differences, and on-farm disease management practices.
References
Lee, S. et al. Evaluation of two high-throughput genotyping systems for rapid identification of Canadian wheat varieties. Canadian Journal of Plant Science. (2023)
Bamforth, J. et al. A survey of Fusarium species and ADON genotype on Canadian wheat grain. Front. Fungal Biol., Sec. Fungal Physiology and Metabolism. (2022)
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