Biology subjects

Belanger, R.

Publications and source records attributed to Belanger, R..

3 recordsLinked to original sources

bioRxiv2023

A new multiplex TaqMan qPCR targeting Clavibacter michiganensis virulence-related genes

Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, is the ability of Cm to infect seeds and plants without causing symptoms what makes it an even more dangerous pathogen. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains and more than 120 samples, including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay was able to screen all Cm strains against other related bacteria. The assay was validated on tissue and seed samples following artificial infection and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves, finding a lower abundance of Cm in the roots compared to the other parts of the plant. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.

microbiology↗

bioRxiv2023

A Hydroponic-Based Bioassay to Facilitate Plasmodiophora brassicae Phenotyping

Clubroot, caused by the obligate parasite Plasmodiophora brassicae, is one of the most devastating diseases affecting the canola/oilseed rape (Brassica napus) industry worldwide. Currently, the planting of clubroot-resistant (CR) cultivars is the most effective strategy used to restrict the spread and the economic losses linked to the disease. However, virulent P. brassicae isolates have been able to infect many of the currently available CR cultivars, and the options to manage the disease are becoming limited. Another challenge has been achieving consistency in evaluating host reactions to P. brassicae infection, with most bioassays conducted in soil and/or potting medium, which requires significant space and can be labour intensive. Visual scoring of clubroot symptom development can also be influenced by user bias. Here, we have developed a hydroponic bioassay using well-characterized P. brassicae single-spore isolates representative of clubroot virulence in Canada, as well as field isolates from three Canadian provinces, in combination with canola inbred homozygous lines carrying resistance genetics representative of CR cultivars available to growers in Canada. To improve the efficiency and consistency of disease assessment, symptom severity scores were compared with clubroot evaluations based on the scanned root area. According to the results, this bioassay offers a reliable, less expensive, and reproducible option to evaluate P. brassicae virulence, as well as a means to identify which canola resistance profile(s) may be effective against particular isolates. This bioassay will contribute to the breeding of new CR canola cultivars and the identification of virulence genes in P. brassicae that could trigger resistance and have been very elusive to this day.

microbiology↗

bioRxiv2023

k-mer-based GWAS enhances the discovery of causal variants and candidate genes in soybean

Genome-wide association studies (GWAS) are powerful statistical methods that detect associations between genotype and phenotype at genome scale. Despite their power, GWAS frequently fail to pinpoint the causal variant or the gene controlling a trait at a given locus in crop species. Assessing genetic variants beyond single-nucleotide polymorphisms (SNPs) could alleviate this problem, for example by including structural variants (SVs). In this study, we tested the potential of SV-and k-mer-based GWAS in soybean by applying these methods to 13 traits. We also performed conventional GWAS analysis based on SNPs and small indels for comparison. We assessed the performance of each GWAS approach based on results at loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes based on the most significantly associated k-mers. Moreover, k-mer-based analyses identified promising candidate genes for loci related to pod color, pubescence form, and resistance to the oomycete Phytophthora sojae. In our dataset, SV-based GWAS did not add value compared to k-mer-based GWAS and may not be worth the time and computational resources required to genotype SVs at population scale. Despite promising results, significant challenges remain regarding the downstream analysis of k-mer-based GWAS. Notably, better methods are needed to associate significant k-mers with sequence variation. Together, our results suggest that coupling k-mer-and SNP/indel-based GWAS is a powerful approach for discovering candidate genes in crop species.

genomics↗